Zenodo.org (152)#
“ZENODO und Co.” Was bringt und wer braucht ein Repositorium?#
Elfi Hesse, Jan-Christoph Deinert, Christian Löschen
Published 2021-01-25
Licensed CC-BY-4.0
Die Online-Veranstaltung fand am 21.01.2021 im Rahmen der SaxFDM-Veranstaltungsreihe “Digital Kitchen - Küchengespräche mit SaxFDM” statt. SaxFDM-Sprecherin Elfi Hesse (HTW Dresden) erläuterte zunächst Grundsätzliches zum Thema Repositorien. Anschließend teilten Nutzer (Jan Deinert – HZDR) und Anbieter (Christian Löschen – TU Dresden/ZIH) lokaler Repositorien ihre Erfahrungen mit uns.
Tags: Research Data Management
Content type: Slides
3D Nuclei annotations and StarDist 3D model(s) (rat brain)#
Romain Guiet
Published 2022-06-15
Licensed CC-BY-4.0
Name: 3D Nuclei annotations and StarDist3D model(s) (rat brain)
Images: From a large tiling acquisition ( https://doi.org/10.5281/zenodo.6646128 ) individual Tile (xyz : 1024x1024x62) were downsampled and cropped (128x128x62). Four crops, from different tiles (./annotations_BIOP/images/) were manually annotated with ITK-SNAP (./annotations_BIOP/masks/)
These four images, and their corresponding masks, were cropped into four quadrants (./crops_BIOP_v1/) in order to get 16 different images (64x64x62).
Conda environment: A conda environment was created using the yml file stardist0.8_TF1.15.yml
Training : Training was performed using the jupyter notebook 1-Training_notebook.ipynb. Three different trainings (with the same random seed, same anisotropy, patch size and grid) were performed and produced three different models (./models/)
Validation images (from the random seed used) were exported to ease the visual inspection of the results(./val_rdm42/).
Validation: To save metrics in a csv file and compare predictions to the annotations the jupyter notebook 2-QC_notebook.ipynb can be used on the validation folder.
Large images: To test the model on larger images one can use Whole_ds441.tif (or Crop_ds441.tif ) These images were obtained using the plugin BigSticher on the raw data ( https://doi.org/10.5281/zenodo.6646128 ), resaved as h5 and exported the downsample by 4 version.
6 Steps Towards Reproducible Research#
Heidi Seibold
Licensed CC-BY-4.0
A short book with 6 steps that get you closer to making your work reproducible.
Tags: Reproducibility, Research Data Management
Content type: Book
A Glimpse of the Open-Source FLIM Analysis Software Tools FLIMfit, FLUTE and napari-flim-phasor-plotter#
Anca Margineanu, Chiara Stringari, Marcelo Zoccoler, Cornelia Wetzker
Published 2024-03-27
Licensed CC-BY-4.0
The presentations introduce open-source software to read in, visualize and analyse fluorescence lifetime imaging microscopy (FLIM) raw data developed for life scientists. The slides were presented at German Bioimaging (GerBI) FLIM Workshop held February 26 to 29 2024 at the Biomedical Center of LMU München by Anca Margineanu, Chiara Stringari and Conni Wetzker.
A journey to FAIR microscopy data#
Stefanie Weidtkamp-Peters, Janina Hanne, Christian Schmidt
Published 2023-05-03
Licensed CC-BY-4.0
Oral presentation, 32nd MoMAN “From Molecules to Man” Seminar, Ulm, online. Monday February 6th, 2023
Abstract:
Research data management is essential in nowadays research, and one of the big opportunities to accelerate collaborative and innovative scientific projects. To achieve this goal, all our data needs to be FAIR (findable, accessible, interoperable, reproducible). For data acquired on microscopes, however, a common ground for FAIR data sharing is still to be established. Plenty of work on file formats, data bases, and training needs to be performed to highlight the value of data sharing and exploit its potential for bioimaging data.
In this presentation, Stefanie Weidtkamp-Peters will introduce the challenges for bioimaging data management, and the necessary steps to achieve data FAIRification. German BioImaging - GMB e.V., together with other institutions, contributes to this endeavor. Janina Hanne will present how the network of imaging core facilities, research groups and industry partners is key to the German bioimaging community’s aligned collaboration toward FAIR bioimaging data. These activities have paved the way for two data management initiatives in Germany: I3D:bio (Information Infrastructure for BioImage Data) and NFDI4BIOIMAGE, a consortium of the National Research Data Infrastructure. Christian Schmidt will introduce the goals and measures of these initiatives to the benefit of imaging scientist’s work and everyday practice.
Abdominal Imaging Window (AIW) for Intravital Imaging#
Michael Gerlach
Published 2024-11-15
Licensed CC-BY-4.0
This upload features a simple model for the creation (Manufacturing/Prototyping) of an abdominal imaging window (AIW) for use in mice intravital microscopy. Manufacture in titanium for chronic implantation. Measures in mm.
Alles meins – oder!? Urheberrechte klären für Forschungsdaten#
Stephan Wünsche
Published 2024-06-04
Licensed CC-BY-4.0
Wem gehören Forschungsdaten? Diese Frage stellt sich bei Daten, an deren Entstehung mehrere Personen beteiligt waren, und besonders bei Textdaten, Bildern und Videos. Hier lernen Sie, für Ihr eigenes Forschungsvorhaben zu erkennen, wessen Urheber- und Leistungsschutzrechte zu berücksichtigen sind. Sie erfahren, wie Sie mit Hilfe von Vereinbarungen frühzeitig Rechtssicherheit herstellen, etwa um Daten weitergeben oder publizieren zu können.
Tags: Research Data Management, Licensing
Content type: Slides
Artificial Blobs and Labels image#
Romain
Published 2023-05-10
Licensed CC-BY-4.0
A groovy script to use in Fiji to generate artificial images and labels, with example images.
Axioscan 7 fluorescent channels not displaying in QuPath#
j
Published 2024-06-25
Hi @ome team,Please find the .czi file attached. When loaded into QuPath using BioFormats, the fluorescence channels populate the brightness/contrast panel but do not show up in the viewer. Re-exporting as OME.Tiff from Zen and loading into QuPath does not help either - the channels do not populate the brightness/contrast panel in this case, and it shows as a RGB image.Please let me know if any further info is needed from me to troubleshoot! Best,J
Bio-Image Data Strudel for Workshop on Research Data Management in TU Dresden Core Facilities#
Cornelia Wetzker
Published 2023-11-08
Licensed CC-BY-4.0
This presentation gives a short outline of the complexity of data and metadata in the bioimaging universe. It introduces NFDI4BIOIMAGE as a newly formed consortium as part of the German ‘Nationale Forschungsdateninfrastruktur’ (NFDI) and its goals and tools for data management including its current members on TU Dresden campus.
Tags: Research Data Management, Tu Dresden, Bioimage Data, Nfdi4Bioimage
Content type: Slide
Bio-image Analysis Code Generation#
Robert Haase
Published 2024-10-28
Licensed CC-BY-4.0
Large Language Models are changing the way we interact with computers, especially how we write code. In this tutorial, we will generate bio-image analysis code using two LLM-based code generators, bia-bob and git-bob. haesleinhuepf/bia-bob haesleinhuepf/git-bob
Bio-image Analysis Code Generation using bia-bob#
Robert Haase
Published 2024-10-09
Licensed CC-BY-4.0
In this presentation I introduce bia-bob, an AI-based code generator that integrates into Jupyter Lab and allows for easy generation of Bio-Image Analysis Python code. It highlights how to get started with using large language models and prompt engineering to get high-quality bio-image analysis code.
Bio-image Analysis with the Help of Large Language Models#
Robert Haase
Published 2024-03-13
Licensed CC-BY-4.0
Large Language Models (LLMs) change the way how we use computers. This also has impact on the bio-image analysis community. We can generate code that analyzes biomedical image data if we ask the right prompts. This talk outlines introduces basic principles, explains prompt engineering and how to apply it to bio-image analysis. We also compare how different LLM vendors perform on code generation tasks and which challenges are ahead for the bio-image analysis community.
Tags: Large Language Models, Python
Content type: Slide
Bio-image Data Science Lectures @ Uni Leipzig / ScaDS.AI#
Robert Haase
Licensed CC-BY-4.0
These are the PPTx training resources for Students at Uni Leipzig who want to dive into bio-image data science with Python. The material developed here between April and July 2024.
Tags: Bioimage Analysis, Deep Learning, Microscopy Image Analysis, Python
Content type: Slides
Building FAIR image analysis pipelines for high-content-screening (HCS) data using Galaxy#
Riccardo Massei, Matthias Berndt, Beatriz Serrano-Solano, Wibke Busch, Stefan Scholz, Hannes Bohring, Jo Nyffeler, Luise Reger, Jan Bumberger, Lucille Lopez-Delisle
Published 2024-11-06
Licensed CC-BY-4.0
Imaging is crucial across various scientific disciplines, particularly in life sciences, where it plays a key role in studies ranging from single molecules to whole organisms. However, the complexity and sheer volume of image data, especially from high-content screening (HCS) experiments involving cell lines or other organisms, present significant challenges. Managing and analysing this data efficiently requires well-defined image processing tools and analysis pipelines that align with the FAIR principles—ensuring they are findable, accessible, interoperable, and reusable across different domains. In the frame of NFDI4BioImaging (the National Research Data Infrastructure focusing on bioimaging in Germany), we want to find viable solutions for storing, processing, analysing, and sharing HCS data. In particular, we want to develop solutions to make findable and machine-readable metadata using (semi)automatic analysis pipelines. In scientific research, such pipelines are crucial for maintaining data integrity, supporting reproducibility, and enabling interdisciplinary collaboration. These tools can be used by different users to retrieve images based on specific attributes as well as support quality control by identifying appropriate metadata. Galaxy, an open-source, web-based platform for data-intensive research, offers a solution by enabling the construction of reproducible pipelines for image analysis. By integrating popular analysis software like CellProfiler and connecting with cloud services such as OMERO and IDR, Galaxy facilitates the seamless access and management of image data. This capability is particularly valuable in bioimaging, where automated pipelines can streamline the handling of complex metadata, ensuring data integrity and fostering interdisciplinary collaboration. This approach not only increases the efficiency of HCS bioimaging but also contributes to the broader scientific community’s efforts to embrace FAIR principles, ultimately advancing scientific discovery and innovation. In the present study, we proposed an automated analysis pipeline for storing, processing, analysing, and sharing HCS bioimaging data. The (semi)automatic workflow was developed by taking as a case study a dataset of zebrafish larvae and cell lines images previously obtained from an automated imaging system generating data in an HCS fashion. In our workflows, images are automatically enriched with metadata (i.e. key-value pairs, tags, raw data, regions of interest) and uploaded to the UFZ-OME Remote Objects (OMERO) server using a novel OMERO tool suite developed with GALAXY. Workflows give the possibility to the user to intuitively fetch images from the local server and perform image analysis (i.e. annotation) or even more complex toxicological analyses (dose response modelling). Furthermore, we want to improve the FAIRness of the protocol by adding a direct upload link to the Image Data Resource (IDR) repository to automatically prepare the data for publication and sharing.
https://zenodo.org/records/14044640
https://doi.org/10.5281/zenodo.14044640
https://galaxyproject.org/news/2024-11-08-galaxy-imaging-fair-pipelines/
Building a FAIR image data ecosystem for microscopy communities#
Isabel Kemmer, Antje Keppler, Beatriz Serrano-Solano, Arina Rybina, Bugra Özdemir, Johanna Bischof, El Ghadraoui, Ayoub, Eriksson, John E., Aastha Mathur
Published 2023-03-31
Licensed CC-BY-4.0
Bioimaging has now entered the era of big data with faster than ever development of complex microscopy technologies leading to increasingly complex datasets. This enormous increase in data size and informational complexity within those datasets has brought with it several difficulties in terms of common and harmonized data handling, analysis and management practices, which are currently hampering the full potential of image data being realized. Here we outline a wide range of efforts and solutions currently being developed by the microscopy community to address these challenges on the path towards FAIR bioimage data. We also highlight how different actors in the microscopy ecosystem are working together, creating synergies that develop new approaches, and how research infrastructures, such as Euro-BioImaging, are fostering these interactions to shape the field.
CZI (Carl Zeiss Image) dataset with artificial test camera images with various dimension for testing libraries reading#
Sebastian Rhode
Published 2022-08-22
Licensed CC-BY-4.0
Set of CZI test images created by using a simulated microscope with a test grayscale camera (no LSM or AiryScan or RGB). The filename indicates the used dimension(s) for the acquisition experiment. The files can be used to test the basic functionality of libraries reading CZI files.
Examples:
S=2_T=3_CH=1.czi = 2 Scenes, 3 TimePoints and 1 Channel
Z-Stack was not activated inside acquisition experiment
S=2_T=3_Z=5_CH=2.czi = 2 Scenes, 3 TimePoints, 5-Z-Planes and 1 Channels
Z-Stack was activated inside acquisition experiment
The test files (so far) contain not any data with more “advanced” dimensions like AiryScan rawdata, illumination angles etc. Also no CZI files with pixel type RGB are included yet.
CZI file examples#
Nicolas Chiaruttini
Published 2023-08-18
Licensed CC-BY-4.0
A set of public CZI files. These can be used for testing CZI readers.
Demo LISH 4x8 15pct 647.czi: A cleared mouse brain acquired with a Zeiss LightSheet Z1 with 32 tiles. Courtesy of the Carl Petersen lab LSENS (https://www.epfl.ch/labs/lsens). Sampled prepared by Yanqi Liu an imaged by Olivier Burri.
test_gray.czi: a synthetically generated CZI file without metadata, made by Sebastian Rhode
Image_1_2023_08_18__14_32_31_964.czi: an example multi-part CZI file, containing only camera noise
a xt scan, xz scan, xzt scan
a set of multi angle, multi illumination, mutli tile acquisition, taken on the LightSheet Z1 microscope of the PTBIOP by Lorenzo Talà
CZI: Open Science Program Collection#
Content type: Collection
Cellpose model for Digital Phase Contrast images#
Laura Capolupo, Olivier Burri, Romain Guiet
Published 2022-02-09
Licensed CC-BY-4.0
Name: Cellpose model for Digital Phase Contrast images
Data type: Cellpose model, trained via transfer learning from ‘cyto’ model.
Training Dataset: Light microscopy (Digital Phase Contrast) and Manual annotations (10.5281/zenodo.5996883)
Training Procedure: Model was trained using a Cellpose version 0.6.5 with GPU support (NVIDIA GeForce RTX 2080) using default settings as per the Cellpose documentation
python -m cellpose –train –dir TRAINING/DATASET/PATH/train –test_dir TRAINING/DATASET/PATH/test –pretrained_model cyto –chan 0 –chan2 0
The model file (MODEL NAME) in this repository is the result of this training.
Prediction Procedure: Using this model, a label image can be obtained from new unseen images in a given folder with
python -m cellpose –dir NEW/DATASET/PATH –pretrained_model FULL_MODEL_PATH –chan 0 –chan2 0 –save_tif –no_npy
Cellpose models for Label Prediction from Brightfield and Digital Phase Contrast images#
Romain Guiet, Olivier Burri
Published 2022-02-25
Licensed CC-BY-4.0
Name: Cellpose models for Brightfield and Digital Phase Contrast images
Data type: Cellpose models trained via transfer learning from the ‘nuclei’ and ‘cyto2’ pretrained model with additional Training Dataset . Includes corresponding csv files with ‘Quality Control’ metrics(§) (model.zip).
Training Dataset: Light microscopy (Digital Phase Contrast or Brightfield) and automatic annotations (nuclei or cyto) (https://doi.org/10.5281/zenodo.6140064)
Training Procedure: The cellpose models were trained using cellpose version 1.0.0 with GPU support (NVIDIA GeForce K40) using default settings as per the Cellpose documentation . Training was done using a Renku environment (renku template).
Command Line Execution for the different trained models
nuclei_from_bf:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model nuclei –img_filter _bf –mask_filter _nuclei –chan 0 –chan2 0 –use_gpu –verbose
cyto_from_bf:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model cyto2 –img_filter _bf –mask_filter _cyto –chan 0 –chan2 0 –use_gpu –verbose
nuclei_from_dpc:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model nuclei –img_filter _dpc –mask_filter _nuclei –chan 0 –chan2 0 –use_gpu –verbose
cyto_from_dpc:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model cyto2 –img_filter _dpc –mask_filter _cyto –chan 0 –chan2 0 –use_gpu –verbose
nuclei_from_sqrdpc:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model nuclei –img_filter _sqrdpc –mask_filter _nuclei –chan 0 –chan2 0 –use_gpu –verbose
cyto_from_sqrdpc:
cellpose –train –dir ‘data/train/’ –test_dir ‘data/test/’ –pretrained_model cyto2 –img_filter _sqrdpc –mask_filter _cyto –chan 0 –chan2 0 –use_gpu –verbose
NOTE (§): We provide a notebook for Quality Control, which is an adaptation of the “Cellpose (2D and 3D)” notebook from ZeroCostDL4Mic .
NOTE: This dataset used a training dataset from the Zenodo entry(https://doi.org/10.5281/zenodo.6140064) generated from the “HeLa “Kyoto” cells under the scope” dataset Zenodo entry(https://doi.org/10.5281/zenodo.6139958) in order to automatically generate the label images.
NOTE: Make sure that you delete the “_flow” images that are auto-computed when running the training. If you do not, then the flows from previous runs will be used for the new training, which might yield confusing results.
ChatGPT for Image Analysis#
Robert Haase
Published 2024-08-25
Licensed CC-BY-4.0
Large Language Models (LLMs) such as ChatGPT are changing the way we interact with computers, including how we analye microscopy imaging data. In this talk I introduce basic concepts of asking LLMs to write code and how to modify the questions to get the best out of it. For trying out these prompt engineering basics there are additional online resources available: https://scads.github.io/prompt-engineering-basics-2024/intro.html
Combining the BIDS and ARC Directory Structures for Multimodal Research Data Organization#
Torsten Stöter, Tobias Gottschall, Andrea Schrader, Peter Zentis, Monica Valencia-Schneider, Niraj Kandpal, Werner Zuschratter, Astrid Schauss, Timo Dickscheid, Timo Mühlhaus, Dirk von Suchodoletz
Licensed CC-BY-4.0
Interdisciplinary collaboration and integrating large, diverse datasets are crucial for answering complex research questions, requiring multimodal data analysis and adherence to FAIR principles. To address challenges in capturing the full research cycle and contextualizing data, DataPLANT developed the Annotated Research Context (ARC), while the neuroimaging community extended the Brain Imaging Data Structure (BIDS) for microscopic image data, both providing standardized, file system-based storage structures for organizing and sharing data with metadata.
Tags: Research Data Management, FAIR-Principles
Content type: Poster
Conference Slides - 4th Day of Intravital Microscopy#
Ishikawa-Ankerhold, Dr. Hellen
Published 2024-11-13
Licensed CC-BY-4.0
Conference Slides for the presentation of GerBI e.V. at the 4th Day of Intravital Microscopy in Leuven, Belgium. Features Structure, activities and Links to join GerBI e.V.
Crashkurs Forschungsdatenmanagement#
Barbara Weiner, Stephan Wünsche, Stefan Kühne, Pia Voigt, Sebastian Frericks, Clemens Hoffmann, Romy Elze, Ronny Gey
Published 2020-04-30
Licensed CC-BY-4.0
Diese Präsentation bietet einen Einstieg in alle relevanten Bereiche des Forschungsdatenmanagements an der Universität Leipzig. Behandelt werden Grundlagen des Forschungsdatenmanagements, technische, ethische und rechtliche Aspekte sowie die Archivierung und Publikation von Forschungsdaten. Die Präsentation enthält zahlreiche weiterführende Links (rot) und Literaturhinweise.
Ergänzend hierzu wird eine Präsentation mit Übungsaufgaben angeboten, die helfen soll, das Gelernte zu festigen und in der eigenen Forschungspraxis umzusetzen. Den Aufgaben folgen jeweils eine Antwortfolie sowie deren Auflösung.
Tags: Research Data Management
Content type: Slides
Creating open computational curricula#
Kari Jordan, Zhian Kamvar, Toby Hodges
Published 2020-12-11
Licensed CC-BY-4.0
In this interactive session, Carpentries team members will guide attendees through three stages of the backward design process to create a lesson development plan for the open source tool of their choosing. Attendees will leave having identified what practical skills they aim to teach (learning objectives), an approach for designing challenge questions (formative assessment), and mechanisms to give and receive feedback.
Content type: Slide
Cultivating Open Training#
Robert Haase
Published 2024-03-14
Licensed CC-BY-4.0
In this SaxFDM Digital Kitchen, I introduced current challenges and potential solutions for openly sharing training materials, softly focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and uploading materials to publicly acessible repositories are proposed to fill this gap.
Tags: Open Science, Research Data Management, FAIR-Principles, Bioimage Analysis, Licensing
Content type: Slides
Cultivating Open Training to advance Bio-image Analysis#
Robert Haase
Published 2024-04-25
Licensed CC-BY-4.0
These slides introduce current challenges and potential solutions for openly sharing training materials, focusing on bio-image analysis. In this field a lot of training materials circulate in private channels, but openly shared, reusable materials, according to the FAIR-principles, are still rare. Using the CC-BY license and publicly acessible repositories are proposed to fill this gap.
Tags: Research Data Management, Licensing, FAIR-Principles
Content type: Slides
DALIA Interchange Format#
Jonathan Geiger, Petra Steiner, Abdelmoneim Amer Desouki, Frank Lange
Published 2024-06-07
Licensed CC-BY-SA-4.0
The DALIA (Data Literacy Alliance) project aims to develop a knowledge graph for FAIR teaching and learning materials on data literacy, data competencies and research data management (RDM) skills within the National Research Data Infrastructure (NFDI) and the RDM landscape. Such a platform thrives on the participation of users who want to search, create, manage or use teaching and learning materials. A schematization of the metadata is necessary for the interoperability of teaching and learning materials. This is done by the DALIA Interchange Format (DIF), which provides a framework for making the metadata of teaching and learning materials transparent, comparable and smooth to integrate into the DALIA platform. It includes the description and explanation of the data fields for the online publication of educational resources. The DIF was developed in close consultation with the scientific community. This development process included several feedback rounds in which valuable feedback was provided and subsequently incorporated into the DIF. This not only contributed to the clear, transparent and user-oriented definitions of the data fields, and to a clear structure, but also to the integration of many existing data standards and to the (special) requirements of the scientific community. The selection of elements is based on the Dublin Core Application Profile. The DIF is provided as a PDF document and in table form (ODS) to convey the attributes of the teaching and learning materials and their definitions in an easily understandable form and to facilitate communication. It also includes a legend and an example in tabular form. In addition, a template (CSV) with the attributes as column headers is provided, which can be used for recording the metadata of the teaching and learning materials. The tables can also be transferred to technical application profiles. We would like to thank all the commentators of the previous versions, especially Susanne Arndt, Sophie Boße, Sonja Felder, Marc Fuhrmans, Jan-Michael Haugwitz, Marina Lemaire, Karoline Lemke, Birte Lindstädt, Juliane Röder, and Jakob Voß. Without their feedback and advice, the DIF would be less transparent.
Data stewardship and research data management tools for multimodal linking of imaging data in plasma medicine#
Ahmadi, Mohsen, Wagner, Robert, Mattern, Philipp, Plathe, Nick, Bekeschus, Sander, Becker, Markus M., Stöter, Torsten, Weidtkamp-Peters, Stefanie
Published 2023-11-03
Licensed CC-BY-4.0
A more detailed understanding of the effect of plasmas on biological systems can be fostered by combining data from different imaging modalities, such as optical imaging, fluorescence imaging, and mass spectrometry imaging. This, however, requires the implementation and use of sophisticated research data management (RDM) solutions to incorporate the influence of plasma parameters and treatment procedures as well as the effects of plasma on the treated targets. In order to address this, RDM activities on different levels and from different perspectives are started and brought together within the framework of the NFDI consortium NFDI4BIOIMAGE.
Datenmanagement#
Robert Haase
Published 2024-04-14
Licensed CC-BY-4.0
In dieser Data Management Session wird der Lebenszyklus von Daten näher beleuchtet. Wie entstehen Daten, was passiert mit ihnen, wenn sie verarbeitet werden? Wem gehören die Daten und wer ist dafür verantwortlich, sie zu veröffentlichen, zu archivieren und gegebenenfalls wiederzuverwenden? Wir werden einen Datenmanagementplan in Gruppenarbeit entwerfen, ggf. mit Hilfe von ChatGPT.
Tags: Research Data Management
Content type: Slides
Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz#
Pia Voigt, Carolin Hundt
Published 2024-04-19
Licensed CC-BY-4.0
Workshop zum Thema „Datenmanagement im Fokus: Organisation, Speicherstrategien und Datenschutz“ auf der Data Week Leipzig Der Umgang mit Daten ist im Alltag nicht immer leicht: Wie und wo speichert man Daten idealerweise? Welche Strategien helfen, den Überblick zu behalten und wie geht man mit personenbezogenen Daten um? Diese Fragen möchten wir gemeinsam mit Ihnen anhand individueller Datenprobleme besprechen und Ihnen Lösungen aufzeigen, wie Sie ihr Datenmanagement effizient gestalten können.
Tags: Research Data Management
Content type: Slides
Datenmanagementpläne erstellen - Teil 1#
Pia Voigt, Barbara Weiner
Published 2021-03-23
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Tags: Research Data Management
Content type: Slides
Datenmanagementpläne erstellen - Teil 2#
Pia Voigt, Barbara Weiner
Published 2021-03-30
Licensed CC-BY-4.0
Was ist ein Datenmanagementplan? Welche Vorgaben sollte ich beachten? Wie erstelle ich einen solchen für mein Forschungsprojekt und welche nützlichen Tools kann ich hierfür verwenden?
Die Anforderungen der Forschungsförderer zum Datenmanagement steigen stetig. Damit verbunden ist häufig auch das Erstellen eines Datenmanagementplans. Dabei erwarten DFG, BMBF oder die EU jeweils unterschiedliche Angaben zur Erhebung, Speicherung und Veröffentlichung von projektbezogenen Forschungsdaten. Zudem bietet das Erstellen eines Datenmanagementplans viele Vorteile und hilft Ihnen nicht zuletzt, die Anforderungen der guten wissenschaftlichen Praxis strukturiert umzusetzen.
Was im ersten Moment unübersichtlich und überfordernd wirkt, soll in diesem Kurs anhand einer grundlegenden theoretischen Einführung im ersten und praxisorientierter Beispiele im zweiten Teil der Veranstaltung handhabbar gemacht werden. Sie lernen, was hinter den Anforderungen der Forschungsförderer steckt, welche Elemente ein Datenmanagementplan enthalten sollte und wie sie einen solchen mithilfe interaktiver Tools selbst erstellen können.
Version 2 enthält aktuelle Links und weiterführende Hinweise zu einzelnen Aspekten eines Datenmanagementplans.
Version 3 ist die überarbeitete und aktualisierte Version der ersten beiden und enthält u.a. Hinweise zur Lizenzierung und zu Nutzungsrechten an Forschungsdaten.
Tags: Research Data Management
Content type: Slides
Deconvolution Test Dataset#
Romain Guiet
Published 2021-07-14
Licensed CC-BY-4.0
This a test dataset, HeLa cells stained for action using Phalloidin-488 acquired on confocal Zeiss LSM710, which contains
Ph488.czi (contains all raw metadata)
Raw_large.tif ( is the tif version of Ph488.czi, provided for conveninence as tif doesn’t need Bio-Formats to be open in Fiji )
Raw.tif , is a crop of the large image
- PSFHuygens_confocal_Theopsf.tif , is a theoretical PSF generated with HuygensPro
- PSFgen_WF_WBpsf.tif , is a theoretical PSF generated with PSF generator
PSFgen_WFsquare_WBpsf.tif, is the result of the square operation on PSFgen_WF_WBpsf.tif , to approximate a confocal PSF
Development of a platform for advanced optics education, training and prototyping#
Nadine Utz, Sabine Reither, Ruth Hans, Christian Feldhaus
Published 2023-10-05
Licensed CC-BY-4.0
In bio-medical research we often need to combine a broad range of expertise to run complex experiments and analyse and interpret their results. Also, it is desirable that all stakeholders of a project understand all parts of the experiment and analysis to draw and support the right conclusions. For imaging experiments this usually requires a basic understanding of the underlying physics. This has not necessarily been part of the professional training of all stakeholders, e.g. biologists or data scientists. Therefore an affordable platform for easily demonstrating and explaining imaging principles would be desirable. Building up on a commercially available STEM Optics kit we developed extensions with widely available and affordable components to demonstrate advanced imaging techniques like e.g. confocal, lightsheet, OPT, spectral imaging. All models are quick and easy to build, yet demonstrate the important physical principles each imaging technique is based on. Further use cases for this kit are training courses, demonstrations for imaging newbies when designing an experiment and outreach activities but also basic level prototyping.
Digital Phase Contrast on Primary Dermal Human Fibroblasts cells#
Laura Capolupo
Published 2022-02-09
Licensed CC-BY-4.0
Name: Digital Phase Contrast on Primary Dermal Human Fibroblasts cells
Data type: Paired microscopy images (Digital Phase Contrast, square rooted) and corresponding labels/masks used for cellpose training (the corresponding Brightfield images are also present), organized as recommended by cellpose documentation.
Microscopy data type: Light microscopy (Digital Phase Contrast and Brighfield )
Manual annotations: Labels/masks obtained via manual segmentation. For each region, all cells were annotated manually. Uncertain objects (Dust, fused cells) were left unannotated, so that the cellpose model (10.5281/zenodo.6023317) may mimic the same user bias during prediction. This was particularly necessary due to the accumulation of floating debris in the center of the well.
Microscope: Perkin Elmer Operetta microscope with a 10x 0.35 NA objective
Cell type: Primary Dermal Human Fibroblasts cells
File format: .tif (16-bit for DPC and 16-bit for the masks)
Image size: 1024x1024 (Pixel size: 634 nm)
NOTE : This dataset was used to train cellpose model ( 10.5281/zenodo.6023317 )
Efficiently starting institutional research data management#
Katarzyna Biernacka, Katrin Cortez, Kerstin Helbig
Published 2019-10-15
Licensed CC-BY-4.0
Researchers are increasingly often confronted with research data management (RDM) topics during their work. Higher education institutions therefore begin to offer services for RDM at some point to give support and advice. However, many groundbreaking decisions have to be made at the very beginning of RDM services. Priorities must be set and policies formulated. Likewise, the staff must first be qualified in order to provide advice and adequately deal with the manifold problems awaiting. The FDMentor project has therefore bundled the expertise of five German universities with different experiences and levels of RDM knowledge to jointly develop strategies, roadmaps, guidelines, and open access training material. Humboldt-Universität zu Berlin, Freie Universität Berlin, Technische Universität Berlin, University of Potsdam, and European University Viadrina Frankfurt (Oder) have worked together on common solutions that are easy to adapt. With funding of the German Federal Ministry of Education and Research, the collaborative project addressed four problem areas: strategy development, legal issues, policy development, and competence enhancement. The aim of the project outcomes is to provide other higher education institutions with the best possible support for the efficient introduction of research data management. Therefore, all project results are freely accessible under the CC-BY 4.0 international license. The early involvement of the community in the form of workshops and the collection of feedback has proven its worth: the FDMentor strategies, roadmaps, guidelines, and training materials are applied and adapted beyond the partner universities.
Tags: Research Data Management
Content type: Document
Einblicke ins Forschungsdatenmanagement - Darf ich das veröffentlichen? Rechtsfragen im Umgang mit Forschungsdaten#
Stephan Wünsche, Pia Voigt
Published 2021-05-11
Licensed CC-BY-4.0
Diese Präsentation wurde im Zuge der digitalen Veranstaltungsreihe “Einblicke ins Forschungsdatenmanagement” erstellt. Diese findet seit dem SS 2020 an der Universität Leipzig für alle Interessierten zu verschiedenen Themen des Forschungsdatenmanagements statt.
Dieser Teil der Reihe dreht sich um Rechtsfragen im Umgang mit Forschungsdaten und deren Bedeutung für die wissenschaftliche Praxis. Sie finden in der vorliegenden Präsentation einen Überblick über relevante Rechtsbereiche sowie Erläuterungen zum Datenschutz, Urheberrecht und den Grundsätzen der guten wissenschaftlichen Praxis mit Fokus auf deren Bedeutung im Forschungsdatenmanagement.
Tags: Research Data Management, Data Protection
Content type: Slides
Engineering a Software Environment for Research Data Management of Microscopy Image Data in a Core Facility#
Kunis
Published 2022-05-30
This thesis deals with concepts and solutions in the field of data management in everyday scientific life for image data from microscopy. The focus of the formulated requirements has so far been on published data, which represent only a small subset of the data generated in the scientific process. More and more, everyday research data are moving into the focus of the principles for the management of research data that were formulated early on (FAIR-principles). The adequate management of this mostly multimodal data is a real challenge in terms of its heterogeneity and scope. There is a lack of standardised and established workflows and also the software solutions available so far do not adequately reflect the special requirements of this area. However, the success of any data management process depends heavily on the degree of integration into the daily work routine. Data management must, as far as possible, fit seamlessly into this process. Microscopy data in the scientific process is embedded in pre-processing, which consists of preparatory laboratory work and the analytical evaluation of the microscopy data. In terms of volume, the image data often form the largest part of data generated within this entire research process. In this paper, we focus on concepts and techniques related to the handling and description of this image data and address the necessary basics. The aim is to improve the embedding of the existing data management solution for image data (OMERO) into the everyday scientific work. For this purpose, two independent software extensions for OMERO were implemented within the framework of this thesis: OpenLink and MDEmic. OpenLink simplifies the access to the data stored in the integrated repository in order to feed them into established workflows for further evaluations and enables not only the internal but also the external exchange of data without weakening the advantages of the data repository. The focus of the second implemented software solution, MDEmic, is on the capturing of relevant metadata for microscopy. Through the extended metadata collection, a corresponding linking of the multimodal data by means of a unique description and the corresponding semantic background is aimed at. The configurability of MDEmic is designed to address the currently very dynamic development of underlying concepts and formats. The main goal of MDEmic is to minimise the workload and to automate processes. This provides the scientist with a tool to handle this complex and extensive task of metadata acquisition for microscopic data in a simple way. With the help of the software, semantic and syntactic standardisation can take place without the scientist having to deal with the technical concepts. The generated metadata descriptions are automatically integrated into the image repository and, at the same time, can be transferred by the scientists into formats that are needed when publishing the data.
Euro-BioImaging Scientific Ambassadors Program#
Beatriz Serrano-Solano
Published 2023-07-25
Licensed CC-BY-4.0
Graduation presentation for the 7th cohort of the Open Seeds mentoring & training program for Open Science ambassadors. The project presented is called “Euro-BioImaging Scientific Ambassadors Program”.
Euro-BioImaging ERIC Annual Report 2022#
Euro-BioImaging ERIC
Published 2023-07-14
Licensed CC-BY-4.0
Euro-BioImaging ERIC is the European landmark research infrastructure for biological and biomedical imaging as recognized by the European Strategy Forum on Research Infrastructures (ESFRI). Euro-BioImaging is the gateway to world-class imaging facilities across Europe. This document is the Euro-BioImaging Annual Report for the year 2022.
Euro-BioImaging’s Guide to FAIR BioImage Data - Practical Tasks#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2024-06-04
Licensed CC-BY-4.0
Hands-on exercises on FAIR Bioimage Data from the interactive online workshop “Euro-BioImaging’s Guide to FAIR BioImage Data 2024” (https://www.eurobioimaging.eu/news/a-guide-to-fair-bioimage-data-2024/). Types of tasks included: FAIR characteristics of a real world dataset Data Management Plan (DMP) Journal Policies on FAIR data sharing Ontology search Metadata according to REMBI scheme (Image from: Sarkans, U., Chiu, W., Collinson, L. et al. REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology. Nat Methods 18, 1418–1422 (2021). https://doi.org/10.1038/s41592-021-01166-8) Matching datasets to bioimage repositories Browsing bioimage repositories
Tags: Bioimage Analysis, FAIR-Principles, Research Data Management
Content type: Slides, Tutorial
Euro-BioImaging’s Template for Research Data Management Plans#
Isabel Kemmer, Euro-BioImaging ERIC
Published 2024-06-04
Licensed CC-BY-4.0
Euro-BioImaging has developed a Data Management Plan (DMP) template with questions tailored to bioimaging research projects. Outlining data management practices in this way ensures traceability of project data, allowing for a continuous and unambiguous flow of information throughout the research project. This template can be used to satisfy the requirement to submit a DMP to certain funders. Regardless of the funder, Euro-BioImaging users are encouraged to provide a DMP and can use this template accordingly. This DMP template is available as a fillable PDF with further instructions and sample responses available by hovering over the fillable fields.
Tags: Bioimage Analysis, FAIR-Principles, Research Data Management
Content type: Collection, Tutorial
Euro-BioImaging/BatchConvert: v0.0.4#
bugraoezdemir
Published 2024-02-19
Licensed CC-BY-4.0
Changes implemented since v0.0.3
Support provided for file paths with spaces. Support provided for globbing filenames from s3 for one-to-one conversion (parse_s3_filenames.py modified). Support provided for single file import from s3 (parse_s3_filenames.py modified). run_conversion.py replaces batchconvert_cli.sh and construct_cli.py, uniting them. Error handling updated for each process
Evident OIR sample files tiles + stitched image - FV 4000#
Nicolas Chiaruttini
Published 2024-09-04
Licensed CC-BY-4.0
The files contained in this repository are confocal images taken with the Evident FV 4000 of a sample containing DAPI and mCherry stains, excited with a 405 nm laser and a 561 nm laser
individual tiles are named tiling-sample-brain-section_A01_G001_{i}.oir
The stiched image is named Stitch_A01_G001 and contains an extra file Stitch_A01_G001_00001
Some metadata like the tiles positions are stored in the extra files (omp2info)
Evident OIR sample files with lambda scan - FV 4000#
Nicolas Chiaruttini
Published 2024-07-18
Licensed CC-BY-4.0
The files contained in this repository are confocal images taken with the Evident FV 4000 of a sample containing DAPI and mCherry stains, excited with the 405 nm laser and images for different emission windows (lambda scan). They are public sample files which goal is to help test edge cases of the bio-formats library (https://www.openmicroscopy.org/bio-formats/), in particular for the proper handling of lambda scans.
DAPI_mCherry_22Lambda-420-630-w10nm-s10nm.oir : 22 planes, each plane is an emission window, starting from 420 nm up to 630 nm by steps of 10 nm DAPI_mCherry_4T_5Lambda-420-630-w10nm-s50nm.oir : 20 planes, 5 lambdas from 420 to 630 nm by steps of 50 nm, 4 timepoints DAPI_mCherry_4Z_5Lambda-420-630-w10nm-s50nm.oir : 20 planes, 5 lambdas from 420 to 630 nm by steps of 50 nm, 4 slices DAPI-mCherry_3T_4Z_5Lambda-420-630-w10nm-s50nm.oir : 60 planes, 5 lambdas from 420 to 630 nm by steps of 50 nm, 4 slices, 3 timepoints
Example Microscopy Metadata JSON files produced using Micro-Meta App to document example microscopy experiments performed at individual core facilities#
Alessandro Rigano, Ulrike Boehm, Claire M. Brown, Joel Ryan, James J. Chambers, Robert A. Coleman, Orestis Faklaris, Thomas Guilbert, Michelle S. Itano, Judith Lacoste, Alex Laude, Marco Marcello, Paula Montero-Llopis, Glyn Nelson, Roland Nitschke, Jaime A. Pimentel, Stefanie Weidtkamp-Peters, Caterina Strambio-De-Castillia
Published 2022-01-15
Licensed CC-BY-4.0
Example Microscopy Metadata (Microscope.JSON and Settings.JSON) files produced using Micro-Meta App to document the Hardware Specifications of example Microscopes and the Image Acquisition Settings utilized to acquire example images as listed in the table below.
For each facility, the dataset contains two JSON files:
Microscope.JSON file (e.g., 01_marcello_uliverpool_cci_zeiss_axioobserz1_lsm710.json)
Settings.JSON file (indicated with the name of the image and with the _AS suffix)
Micro-Meta App was developed as part of a global community initiative including the 4D Nucleome (4DN) Imaging Working Group, BioImaging North America (BINA) Quality Control and Data Management Working Group, and QUAlity and REProducibility for Instrument and Images in Light Microscopy (QUAREP-LiMi), to extend the Open Microscopy Environment (OME) data model.
The works of this global community effort resulted in multiple publications featured on a recent Nature Methods FOCUS ISSUE dedicated to Reporting and reproducibility in microscopy.
Learn More! For a thorough description of Micro-Meta App consult our recent Nature Methods and BioRxiv.org publications!
Nr.
Manufacturer
Model
Tier
Εxperiment Type
Facility Name
Department and Institution
URL
References
1
Carl Zeiss Microscopy
Axio Observer Z1 (with LSM 710 scan head)
1
3D visualization of superhydrophobic polymer-nanoparticles
Centre for Cell Imaging (CCI)
University of Liverpool
https://cci.liv.ac.uk/equipment_710.html
Upton et al., 2020
2
Carl Zeiss Microscopy
Axio Observer (Axiovert 200M)
2
Μeasurement of illumination stability on Chinese Hamster Ovary cells expressing Paxillin-EGFP
Advanced BioImaging Facility (ABIF).
McGill University
https://www.mcgill.ca/abif/equipment/axiovert-1
Kiepas et al., 2020
3
Carl Zeiss Microscopy
Axio Observer Z1 (with Spinning Disk)
2
Immunofluorescence imaging of cryosection of Mouse kidney
Imagerie Cellulaire; Quality Control managed by Miacellavie (https://miacellavie.com/)
Centre de recherche du Centre Hospitalier Université de Montréal (CR CHUM), University of Montreal
https://www.chumontreal.qc.ca/crchum/plateformes-et-services (the web site is for all core facilities, not specifically for the core facility hosting this microscope)
Pilliod et al., 2020
4
Carl Zeiss Microscopy
Axio Imager Z2 (with Apotome)
2
Immunofluorescence imaging of mitotic division in Hela cells using
Bioimaging Unit
Newcastle University
https://www.ncl.ac.uk/bioimaging/
Watson et al., 2020
5
Carl Zeiss Microscopy
Axio Observer Z1
2
Fluorescence microscopy of human skin fibroblasts from Glycogen Storage Disease patients.
Life Imaging Center (LIC)
Centre for Integrative Signalling Analysis (CISA), University of Freiburg
https://miap.eu/equipments/sd-i-abl/
Hannibal et al., 2020
6
Leica Microsystems
DMI6000B
2
3D immunofluorescence imaging rhinovirus infected macrophages
IMAG'IC Confocal Microscopy Facility
Institut Cochin, CNRS, INSERM, Université de Paris
https://www.institutcochin.fr/core_facilities/confocal-microscopy/cochin-imaging-photonic-microscopy/organigram_team/10054/view
Jubrail et al., 2020
7
Leica Microsystems
DM5500B
2
Immunofluorescence analysis of the colocalization of PML bodies with DNA double-strand breaks
Bioimaging Unit
Edwardson Building on the Campus for Ageing and Vitality, Newcastle University
https://www.ncl.ac.uk/bioimaging/equipment/leica-dm5500/#overview
da Silva et al., 2019; Nelson et al., 2012
8
Leica Microsystems
DMI8-CS (with TCS SP8 STED 3X)
2
Live-cell imaging of N. benthamiana leaves cells-derived protoplasts
Center for Advanced Imaging (CAi)
School of Mathematics/Natural Sciences, Heinrich-Heine-Universität Düsseldorf
https://www.cai.hhu.de/en/equipment/super-resolution-microscopy/leica-tcs-sp8-sted-3x
Singer et al., 2017; Hänsch et al., 2020
9
Nikon Instruments
Eclipse Ti
2
Immunofluorescence analysis of the cytoskeleton structure in COS cells
Advanced Imaging Center (AIC)
Janelia Research Campus, Howard Hughes Medical Institute
https://www.janelia.org/support-team/light-microscopy/equipment
Abdelfattah et al., 2019; Qian et al., 2019; Grimm et al., 2020
10
Nikon Instruments
Eclipse Ti-E (HCA)
2
Τime-lapse analysis of the bursting behavior of amine-functionalized vesicular assemblies
Light Microscopy Facility (IALS-LIF)
Institute for Applied Life Sciences, University of Massachusetts at Amherst
https://www.umass.edu/ials/light-microscopy
Fernandez et al., 2020
11
Nikon Instruments/Coleman laboratory (customized)
TIRF HILO Epifluorescence light Microscope (THEM)/ Eclipse Ti
2
Single-particle tracking of Halo-tagged PCNA in Lox cells
Coleman laboratory
Anatomy and Structural Biology Department, The Albert Einstein College of Medicine
https://einsteinmed.org/faculty/12252/robert-coleman/
Drosopoulos et al., 2020
12
Nikon Instruments
Eclipse Ti (with Andor Dragon Fly Spinning Disk)
2
Investigation of the 3D structure of cerebral organoids
Montpellier Resources Imagerie
Centre de Recherche de Biologie cellulaire de Montpellier (MRI-CRBM), CNRS, Univerity of Montpellier
https://www.mri.cnrs.fr/en/optical-imaging/our-facilities/mri-crbm.html
Ayala-Nunez et al., 2019
13
Nikon Instruments
Eclipse Ti2
2
Ιmmunofluorescence imaging of cryosections of mouse hearth myocardium
Neuroscience Center Microscopy Core
Neuroscience Center, University of North Carolina
https://www.med.unc.edu/neuroscience/core-facilities/neuro-microscopy/
Aghajanian et al., 2021
14
Nikon Instruments
Eclipse Ti2
2
Live-cell imaging of bacterial cells expressing GFP-PopZ
Microscopy Resources on the North Quad (MicRoN)
Harvard Medical School
https://micron.hms.harvard.edu/
Lim and Bernhardt 2019; Lim et al., 2019
15
Olympus/Biomedical Imaging Group (customized)
TIRF Epifluorescence Structured light Microscope (TESM)/IX71
3
3D distribution of HIV-1 in the nucleus of human cells
Biomedical Imaging Group
Program in Molecular Medicine, University of Massachusetts Medical School
https://trello.com/b/BQ8zCcQC/tirf-epi-fluorescence-structured-light-microscope
Navaroli et al., 2012
16
Olympus/Computer Vision Laboratory (customized)
3D BrightField Scanner/IX71
3
Transmitted light brightfield visualization of swimming spermatocytes
Laboratorio Nacional de Microscopia Avanzada (LNMA) and Computer Vision Laboratory of the Institute of Biotechnology
Universidad Nacional Autonoma de Mexico (UNAM)
https://lnma.unam.mx/wp/
Pimentel et al., 2012; Silva-Villalobos et al., 2014
Getting started
Use these videos to get started with using Micro-Meta App after installation into OMERO and downloading the example data files:
Video 1
Video 2
More information
For full information on how to use Micro-Meta App please utilize the following resources:
Micro-Meta App website
Full documentation
Installation instructions
Step-by-Step Instructions
Tutorial Videos
Background
If you want to learn more about the importance of metadata and quality control to ensure full reproducibility, quality and scientific value in light microscopy, please take a look at our recent publications describing the development of community-driven light 4DN-BINA-OME Microscopy Metadata specifications Nature Methods and BioRxiv.org and our overview manuscript entitled A perspective on Microscopy Metadata: data provenance and quality control.
Example Operetta Dataset#
Nicolas Chiaruttini
Published 2023-07-17
Licensed CC-BY-4.0
This is a microscopy image dataset generated by the Perkin Elmer Operetta HCS microscope by of the user of the PTBIOP EPFL facility.
As of the 17th of July 2023, opening this file in ImageJ/Fiji using the BioFormats 6.14 library, this dataset generates a Null Pointer Exception.
A post on forum.image.sc is linked to this issue:
Excel template for adding Key-Value Pairs to images#
Thomas Zobel, Jens Wendt
Published 2024-10-30
Licensed CC-BY-4.0
This Excel Workbook contains some simple Macros to help with the generation of a .csv in the necessary format for Key-Value pair annotations of images in OMERO. The format is tailored for the OMERO.web script “KeyVal_from_csv.py” (from the version <=5.8.3 of the core omero-scripts). Attached is also a video of Thomas Zobel, the head of the imaging core facility Uni Münster, showcasing the use of the Excel workbook.The video uses a slightly older version of the workbook and OMERO, but the core functionality remains unchanged. Please keep in mind, that the OMERO.web script(s) to handle Key-Value Pairs from/to .csv files will undergo a major change very soon.This might break the compatibility with the format used now for the generated .csv from the workbook.
Forschungsdatenmanagement zukunftsfest gestalten – Impulse für die Strukturevaluation der Nationalen Forschungsdateninfrastruktur (NFDI)#
Steuerungsgremium Allianz-Schwerpunkt, Alexander von Humboldt Foundation, Deutsche Forschungsgemeinschaft, Fraunhofer Society, German Rectors’ Conference, Leibniz Association, German National Academy of Sciences Leopoldina, German Academic Exchange Service, Helmholtz Association of German Research Centres, Max Planck Society
Published 2024-11-04
Licensed CC-BY-4.0
Arbeitspapier des Steuerungsgremiums des Allianz-Schwerpunkts “Digitalität in der Wissenschaft”
From Cells to Pixels: Bridging Biologists and Image Analysts Through a Common Language#
Elnaz Fazeli, Haase Robert, Doube Michael, Miura Kota, Legland David
Published 2024-08-16
Licensed CC-BY-4.0
Bioimaging has transformed our understanding of biological processes, yet extracting meaningful information from complex datasets remains a challenge, particularly for early career scientists. This paper proposes a simplified, systematic approach to bioimage analysis, focusing on categorizing commonly observed structures and shapes, and providing relevant analysis methods. Our approach includes illustrative examples and a visual flowchart, enabling researchers to define analysis objectives clearly. By understanding the diversity of bioimage structures and aligning them with appropriate analysis approaches, the framework empowers researchers to navigate bioimage datasets more efficiently. It also aims to foster a common language between researchers and analysts, thereby enhancing mutual understanding and facilitating effective communication.
GerBI-Chat: Teil 1 - Vom Bedarf bis zum Großgeräteantrag-Schreiben#
Financial & Legal Framework of Core Facilities, Elmar Endl, Jana Hedrich, Juliane Hoth, Julia Nagy, Astrid Schauss, Nina Schulze, Silke Tulok
Published 2024-09-11
Licensed CC-BY-4.0
Die GermanBioImaging (GerBI-GMB) - Deutsche Gesellschaft für Mikroskopie und Bildanalyse e.V. bietet über regelmäßig stattfindende Treffen (GerBI-Chats) die Möglichkeit zum aktiven Austausch der Mitglieder untereinander. Das GerBI-GMB Team “Legal und Finacial Framwork”, welches sich mit administrativen Aufgaben rund um das Core Facility Management beschäftigt, nutzt diese Möglichkeit zum aktiven Austausch innerhalb des Netzwerkes und darüber hinaus. Der Beschaffungsprozess von Forschungsgroßgeräten ist komplex und je nach Institution unterschiedlich geregelt. Aus unserer Sicht lässt sich dieser Prozess grob in drei Stufen aufteilen:
Bedarfsanmeldung Antragsvorbereitung und -fertigstellung Antragsbewilligung und Nutzung
Dieser hier enthaltene Beitrag ist der Initialvortrag des GerBi-Chats zum Teil 1 - Von der Bedarfsanmeldung bis zum Beginn der Antragststellung. Die weiteren Stufen der Großgerätebeschaffung werden in nachfolgenden Beiträgen behandelt.
GerBI-Chat: Teil 2 - Wie schreibe ich am besten einen Großegräteantrag#
Financial & Legal Framework of Core Facilities, Elmar Endl, Jana Hedrich, Juliane Hoth, Julia Nagy, Astrid Schauss, Nina Schulze, Silke Tulok
Published 2024-10-02
Licensed CC-BY-4.0
Die GermanBioImaging (GerBI-GMB) - Deutsche Gesellschaft für Mikroskopie und Bildanalyse e.V. bietet über regelmäßig stattfindende Treffen (GerBI-Chats) die Möglichkeit zum aktiven Austausch der Mitglieder untereinander. Das GerBI-GMB Team “Legal und Finacial Framwork”, welches sich mit administrativen Aufgaben rund um das Core Facility Management beschäftigt, nutzt diese Möglichkeit zum aktiven Austausch innerhalb des Netzwerkes und darüber hinaus. Der Beschaffungsprozess von Forschungsgroßgeräten ist komplex und je nach Institution unterschiedlich geregelt. Aus unserer Sicht lässt sich dieser Prozess grob in drei Stufen aufteilen:
Bedarfsanmeldung Antragsvorbereitung und -fertigstellung Antragsbewilligung und Nutzung
Nach dem Initialvortrag der GerBI-Chat Reihe, in dem das Thema Bedarfsanmeldung im Fokus stand, geht es im hier enthaltenen zweiten Teil „Antragsvorbereitung und -fertigstellung: Wie schreibe ich am besten einen Großgeräteantrag?“ um die Beantragung von Forschungsgroßgeräten nach Art. 91b GG.
Getting started with Python: intro and set-up a conda environment#
Riccardo Massei
Published 2024-10-09
Licensed CC-BY-4.0
YMIA python event 2024 Presentation : “Getting started with Python: intro and set-up a conda environment with Dr. Riccardo Massei”
Gut Analysis Toolbox#
Luke Sorensen, Ayame Saito, Sabrina Poon, Noe Han, Myat, Ryan Hamnett, Peter Neckel, Adam Humenick, Keith Mutunduwe, Christie Glennan, Narges Mahdavian, JH Brookes, Simon, M McQuade, Rachel, PP Foong, Jaime, Estibaliz Gómez-de-Mariscal, Muñoz Barrutia, Arrate, Kaltschmidt, Julia A., King, Sebastian K., Robert Haase, Simona Carbone, A. Veldhuis, Nicholas, P. Poole, Daniel, Pradeep Rajasekhar
Published 2024-09-10
Licensed CC-BY-4.0
What’s Changed
Updating User Dialogs by @mattyrowey in pr4deepr/GutAnalysisToolbox#18 Added Dialog Boxes and Grammar Corrections by @mattyrowey in pr4deepr/GutAnalysisToolbox#19 Updated Dialog Prompts for Clarity by @mattyrowey in pr4deepr/GutAnalysisToolbox#20 Batch analysis option added. fixed a bunch of bugs related to ganglia segmentation and user workflow
New Contributors
@mattyrowey made their first contribution in pr4deepr/GutAnalysisToolbox#18
Full Changelog: https://github.com/pr4deepr/GutAnalysisToolbox/compare/v0.6…v0.7
Gut Analysis Toolbox: Training data and 2D models for segmenting enteric neurons, neuronal subtypes and ganglia#
Luke Sorensen, Ayame Saito, Sabrina Poon, Myat Noe Han, Adam Humenick, Peter Neckel, Keith Mutunduwe, Christie Glennan, Narges Mahdavian, Simon JH Brookes, Rachel M McQuade, Jaime PP Foong, Sebastian K. King, Estibaliz Gómez-de-Mariscal, Arrate Muñoz-Barrutia, Robert Haase, Simona Carbone, Nicholas A. Veldhuis, Daniel P. Poole, Pradeep Rajasekhar
Published 2022-02-15
Licensed CC-BY-4.0
This upload is associated with the software, Gut Analysis Toolbox (GAT). If you use it please cite: Sorensen et al. Gut Analysis Toolbox: Automating quantitative analysis of enteric neurons. J Cell Sci 2024; jcs.261950. doi: https://doi.org/10.1242/jcs.261950 The upload contains StarDist models for segmenting enteric neurons in 2D, enteric neuronal subtypes in 2D and UNet model for enteric ganglia in 2D in gut wholemount tissue. GAT is implemented in Fiji, but the models can be used in any software that supports StarDist and the use of 2D UNet models. The files here also consist of Python notebooks (Google Colab), training and test data as well as reports on model performance. The model files are located in the respective folders as zip files. The folders have also been zipped:
Neuron (Hu; StarDist model):
Main folder: 2D_enteric_neuron_model_QA.zip Model File:2D_enteric_neuron_v4_1.zip
Neuronal subtype (StarDist model):
Main folder: 2D_enteric_neuron_subtype_model_QA.zip Model File: 2D_enteric_neuron_subtype_v4.zip
Enteric ganglia (2D UNet model; Use in FIJI with deepImageJ)
Main folder: 2D_enteric_ganglia_model_QA.zip Model File: 2D_Ganglia_RGB_v2.bioimage.io.model.zip (Compatible with deepimageJ v3)
For the all models, files included are:
Model for segmenting cells or ganglia in 2D FIJI. StarDist or 2D UNet. Training and Test datasets used for training. Google Colab notebooks used for training and quality assurance (ZeroCost DL4Mic notebooks). Quality assurance reports generated from above notebooks. StarDist model exported for use in QuPath.
The model files can be used within can be used within the software, StarDist. They are intended to be used within FIJI or QuPath, but can be used in any software that supports the implementation of StarDist in 2D. Data: All the images were collected from 4 different research labs and a public database (SPARC database) to account for variations in image acquisition, sample preparation and immunolabelling. For enteric neurons the pan-neuronal marker, Hu has been used and the 2D wholemounts images from mouse, rat and human tissue. For enteric neuronal subtypes, 2D images for nNOS, MOR, DOR, ChAT, Calretinin, Calbindin, Neurofilament, CGRP and SST from mouse tissue have been used.. 25 images were used from the following entries in the SPARC database:
Howard, M. (2021). 3D imaging of enteric neurons in mouse (Version 1) [Data set]. SPARC Consortium. Graham, K. D., Huerta-Lopez, S., Sengupta, R., Shenoy, A., Schneider, S., Wright, C. M., Feldman, M., Furth, E., Lemke, A., Wilkins, B. J., Naji, A., Doolin, E., Howard, M., & Heuckeroth, R. (2020). Robust 3-Dimensional visualization of human colon enteric nervous system without tissue sectioning (Version 1) [Data set]. SPARC Consortium. Wang, L., Yuan, P.-Q., Gould, T. and Tache, Y. (2021). Antibodies Tested in theColon – Mouse (Version 1) [Data set]. SPARC Consortium. doi:10.26275/i7dl-58h
The images have been acquired using a combination different microscopes. The images for the mouse tissue were acquired using:
Leica TCS-SP8 confocal system (20x HC PL APO NA 1.33, 40 x HC PL APO NA 1.3)
Leica TCS-SP8 lightning confocal system (20x HC PL APO NA 0.88)
Zeiss Axio Imager M2 (20X HC PL APO NA 0.3)
Zeiss Axio Imager Z1 (10X HC PL APO NA 0.45)
Human tissue images were acquired using:
IX71 Olympus microscope (10X HC PL APO NA 0.3)
For more information, visit the Documentation website. NOTE: The images for enteric neurons and neuronal subtypes have been rescaled to 0.568 µm/pixel for mouse and rat. For human neurons, it has been rescaled to 0.9 µm/pixel . This is to ensure the neuronal cell bodies have similar pixel area across images. The area of cells in pixels can vary based on resolution of image, magnification of objective used, animal species (larger animals -> larger neurons) and potentially how the tissue is stretched during wholemount preparation Average neuron area for neuronal model: 701.2 ± 195.9 pixel2 (Mean ± SD, 6267 cells) Average neuron area for neuronal subtype model: 880.9 ± 316 pixel2 (Mean ± SD, 924 cells) Software References: Stardist Schmidt, U., Weigert, M., Broaddus, C., & Myers, G. (2018, September). Cell detection with star-convex polygons. In International Conference on Medical Image Computing and Computer-Assisted Intervention (pp. 265-273). Springer, Cham. deepImageJ Gómez-de-Mariscal, E., García-López-de-Haro, C., Ouyang, W., Donati, L., Lundberg, E., Unser, M., Muñoz-Barrutia, A. and Sage, D., 2021. DeepImageJ: A user-friendly environment to run deep learning models in ImageJ. Nature Methods, 18(10), pp.1192-1195. ZeroCost DL4Mic von Chamier, L., Laine, R.F., Jukkala, J., Spahn, C., Krentzel, D., Nehme, E., Lerche, M., Hernández-Pérez, S., Mattila, P.K., Karinou, E. and Holden, S., 2021. Democratising deep learning for microscopy with ZeroCostDL4Mic. Nature communications, 12(1), pp.1-18.
Hackaton Results - Conversion of KNIME image analysis workflows to Galaxy#
Riccardo Massei
Published 2024-03-07
Licensed CC-BY-4.0
Results of the project “Conversion of KNIME image analysis workflows to Galaxy” during the Hackathon “Image Analysis in Galaxy” (Freiburg 26 Feb - 01 Mar 2024)
HeLa “Kyoto” cells under the scope#
Romain Guiet
Published 2022-02-25
Licensed CC-BY-4.0
Name: HeLa “Kyoto” cells under the scope
Microscope: Perkin Elmer Operetta microscope with a 20x N.A. 0.8 objective and an Andor Zyla 5.5 camera.
Microscopy data type: The time-lapse datasets were acquired every 15 minutes, for 60 hours. From the individual plan images (channels, time-points, field of view exported by the PerkinElmer software Harmony) multi-dimension images were generated using the Operetta_Importer-0.1.21 with a downscaling of 4.
Channel 1 : Low Contrast DPC (Digital Phase Contrast)
Channel 2 : High Contrast DPC
Channel 3 : Brightfield
Channel 4 : EGFP-α-tubulin
Channel 5 : mCherry-H2B
File format: .tif (16-bit)
Image size: 540x540 (Pixel size: 0.299 nm), 5c, 1z , 240t
Cell type: HeLa “Kyoto” cells, expressing EGFP-α-tubulin and mCherry-H2B ( Schmitz et al, 2010 )
Protocol: Cells were resuspended in Imaging media and were seeded in a microscopy grade 96 wells plate ( CellCarrier Ultra 96, Perkin Elmer). The day after seeding, and for 60 hours, images were acquired in 3 wells, in 25 different fields of view, every 15 minutes.
Imaging media: DMEM red-phenol-free media (FluoroBrite™ DMEM, Gibco) complemented with Fetal Calf Serum and Glutamax.
NOTE: This dataset was used to automatically generate label images in the following Zenodo entry: https://doi.org/10.5281/zenodo.6140064
NOTE: This dataset was used to train the cellpose models in the following Zenodo entry: https://doi.org/10.5281/zenodo.6140111
High throughput & automated data analysis and data management workflow with Cellprofiler and OMERO#
Sarah Weischer, Jens Wendt, Thomas Zobel
Licensed CC-BY-4.0
In this workshop a fully integrated data analysis solutions employing OMERO and commonly applied image analysis tools (e.g., CellProfiler, Fiji) using existing python interfaces (OMERO Python language bindings, ezOmero, Cellprofiler Python API) is presented.
Tags: OMERO, Data Analysis, Bioimage Analysis
Content type: Collection
Human DAB staining Axioscan BF 20x#
Mario Garcia
Published 2024-05-21
Licensed CC-BY-4.0
Human brain tissue with DAB immunostaining. Image acquired by BF microscopy in Zeiss Axioscan at 20x.
I3D:bio’s OMERO training material: Re-usable, adjustable, multi-purpose slides for local user training#
Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Carsten Fortmann-Grote, Julia Dohle, Peter Zentis, Niraj Kandpal, Susanne Kunis, Thomas Zobel, Stefanie Weidtkamp-Peters, Elisa Ferrando-May
Published 2023-11-13
Licensed CC-BY-4.0
The open-source software OME Remote Objects (OMERO) is a data management software that allows storing, organizing, and annotating bioimaging/microscopy data. OMERO has become one of the best-known systems for bioimage data management in the bioimaging community. The Information Infrastructure for BioImage Data (I3D:bio) project facilitates the uptake of OMERO into research data management (RDM) practices at universities and research institutions in Germany. Since the adoption of OMERO into researchers’ daily routines requires intensive training, a broad portfolio of training resources for OMERO is an asset. On top of using the OMERO guides curated by the Open Microscopy Environment Consortium (OME) team, imaging core facility staff at institutions where OMERO is used often prepare additional material tailored to be applicable for their own OMERO instances. Based on experience gathered in the Research Data Management for Microscopy group (RDM4mic) in Germany, and in the use cases in the I3D:bio project, we created a set of reusable, adjustable, openly available slide decks to serve as the basis for tailored training lectures, video tutorials, and self-guided instruction manuals directed at beginners in using OMERO. The material is published as an open educational resource complementing the existing resources for OMERO contributed by the community.
Tags: OMERO, Research Data Management, Nfdi4Bioimage, I3Dbio
Content type: Slide, Video
https://zenodo.org/records/8323588
https://www.youtube.com/playlist?list=PL2k-L-zWPoR7SHjG1HhDIwLZj0MB_stlU
ICS/IDS stitched file#
IMCF
Published 2024-06-13
Licensed CC-BY-4.0
Hi @ome team ! We usually use ICS/IDS file formats as an output to our stitching pipeline as the reading and writing is pretty fast. However, it seems that since Bio-Formats 7.x opening the files is not working anymore. I tried with a Fiji with Bio-Formats 6.10.1 and the files open, but more recent versions give an issue. java.lang.NullPointerException at loci.formats.in.ICSReader.initFile(ICSReader.java:1481) at loci.formats.FormatReader.setId(FormatReader.java:1480) at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498) at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141) at loci.plugins.in.Importer.showDialogs(Importer.java:156) at loci.plugins.in.Importer.run(Importer.java:77) at loci.plugins.LociImporter.run(LociImporter.java:78) at ij.IJ.runUserPlugIn(IJ.java:244) at ij.IJ.runPlugIn(IJ.java:210) at ij.Executer.runCommand(Executer.java:152) at ij.Executer.run(Executer.java:70) at ij.IJ.run(IJ.java:326) at ij.IJ.run(IJ.java:337) at ij.macro.Functions.doRun(Functions.java:703) at ij.macro.Functions.doFunction(Functions.java:99) at ij.macro.Interpreter.doStatement(Interpreter.java:281) at ij.macro.Interpreter.doStatements(Interpreter.java:267) at ij.macro.Interpreter.run(Interpreter.java:163) at ij.macro.Interpreter.run(Interpreter.java:93) at ij.macro.MacroRunner.run(MacroRunner.java:146) at java.lang.Thread.run(Thread.java:750)
You can find one example file at this link 1. Thanks for your help !Best,Laurent
Image Repository Decision Tree - Where do I deposit my imaging data#
Kemmer, Isabel, Romdhane, Feriel, Euro-BioImaging ERIC
Published 2024-10-22
Licensed CC-BY-4.0
Depositing data in quality data repositories is one crucial step towards FAIR (Findable, Accessible, Interoperable, and Reusable) data. Accordingly, Euro-BioImaging strongly encourages sharing scientific imaging data in established, thematic repositories. To guide you in the selection of appropriate repositories, we have created an overview of available repositories for different types of image data, including their scope and requirements. This decision tree guides you through questions about your data and directs you to the correct repository, and/or provides instructions for further processing to meet the critera of the repositories. Three seperate trees are provided for different classes of imaging data: open bioimage data, preclinical data, and human imaging data.
ImageJ tool for percentage estimation of pneumonia in lungs#
Martin Schätz, Olga Rubešová, Jan Mareš, Alan Spark
Published 2023-05-02
Licensed CC-BY-4.0
The software tool is developed on demand of Radiological Department of Faculty Hospital of Královské Vinohrady, with the aim to provide a tool to estimate the percentage of pneumonia (or COVID-19 presence) in lungs. Paper Estimation of Covid-19 lungs damage based on computer tomography images analysis presenting the tool is available on F1000reserach DOI: 10.12688/f1000research.109020.1. The underlying dataset is published in Zenodo (DOI:10.5281/zenodo.5805939). One of the challenges was to design a tool that would be available without complicated install procedures and would process data in a reasonable time even on office computers. For this reason, 8-bit and 16-bit version of the tool exists. The FIJI software (or ImageJ with Bio-Formats plugin installed) was selected as the best candidate. Examples of use and tutorials are available at GitHub.
Underlying data: DOI:10.5281/zenodo.5805939 The first five datasets are analyzed using this tool, with results and parameters to repeat the analysis in results_csv.csv or results.xlsx.
Contributions: Martin SCHÄTZ: Coding, tool testing, data curation, data set analysis Olga RUBEŠOVÁ: Code review, tutorial preparation, tool testing, data set analysis Jan MAREŠ: Tool testing, data set analysis Alan SPARK: Tool testing
The work was funded by the Ministry of Education, Youth and Sports by grant ‘Development of Advanced Computational Algorithms for evaluating post-surgery rehabilitation’ number LTAIN19007. The work was also supported from the grant of Specific university research – grant No FCHI 2022-001.
Implantation of abdominal imaging windows on the mouse kidney#
Michael Gerlach
Published 2024-09-04
Licensed CC-BY-ND-4.0
This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen). Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation. This upload contains the full version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.
Implantation of abdominal imaging windows on the mouse kidney - short version#
Michael Gerlach
Published 2024-09-09
Licensed CC-BY-ND-4.0
This video describes the surgical process of implanting an abdominal imaging window (AIW) on the kidney of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen). Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation. This upload contains the shortened version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.
Implantation of abdominal imaging windows on the mouse liver#
Michael Gerlach
Published 2024-09-04
Licensed CC-BY-ND-4.0
This video describes the surgical process of implanting an abdominal imaging window (AIW) on the liver of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen). Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation. This upload contains the full version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.
Implantation of abdominal imaging windows on the mouse liver - short version#
Michael Gerlach
Published 2024-09-09
Licensed CC-BY-ND-4.0
This video describes the surgical process of implanting an abdominal imaging window (AIW) on the liver of mice. This window can be used for acute or longitudinal imaging. All experiments have been reviewed and approved by the local authorities (Landesdirektion Sachsen). Implantation of chronic abdominal windows allows for microscopical investigation of highly dynamic processes in physiological and pathological circumstances and is generally tolerated well by experimental animals. It enables insights which otherwise could only be obtained using high numbers of experimental animals. The method can be regarded as reduction approach in terms of 3R implementation. This upload contains the short version and is distributed under CC BY-ND 4.0 license to inhibit decontextualized misuse. Please check license terms for usage, especially for remixing/transforming! If you want to remix the material, get in contact with the author.
Ink in a dish#
Cavanagh
Published 2024-09-03
Licensed CC-ZERO
A test data set for troublshooting. no scientific meaning.
Insights and Impact From Five Cycles of Essential Open Source Software for Science#
Kate Hertweck, Carly Strasser, Dario Taraborelli
Licensed CC-BY-4.0
Open source software (OSS) is essential for advancing scientific discovery, particularly in biomedical research, yet funding to support these vital tools has been limited. The Chan Zuckerberg Initiative’s Essential Open Source Software for Science (EOSS) program has significantly contributed to this field by providing $51.8 million in funding over five years to support the maintenance, growth, and community engagement of critical OSS tools. The program has impacted scientific OSS projects by improving their technical outputs, community building, and sustainability practices, and fostering collaborations within the OSS community. Additionally, EOSS funding has enhanced diversity, equity, and inclusion within the OSS community, although changes in principal investigator demographics were not observed. The funded projects have had a substantial impact on biomedical research by improving the usability and accessibility of scientific software, which has led to increased adoption and advancements in various biomedical fields.
Tags: Open Source Software, Funding, Sustainability
Content type: Publication
Insights from Acquiring Open Medical Imaging Datasets for Foundation Model Development#
Stefan Dvoretskii
Published 2024-04-10
Licensed CC-BY-4.0
Insights from Acquiring Open Medical Imaging Datasets for Foundation Model Development#
Stefan Dvoretskii
Published 2024-04-10
Licensed CC-BY-4.0
Institutionalization and Collaboration as a Way of Addressing the Challenges Open Science Presents to Libraries: The University of Konstanz as a National Pioneer#
Sophie Habinger, Maximilian Heber, Sonja Kralj, Emilia Mikautsch
Published 2024-07-09
Licensed CC-BY-4.0
The rise of Open Science (OS) and the academic community’s needs that come with it bring about a range of challenges for academic libraries. To face these challenges, the University of Konstanz has created a competence unit called Team Open Science in the Communication, Information, Media Center (KIM) - a joint unit of library and IT infrastructure. The Team creates synergies within itself and across the library. In December 2023, it involved 12 staff members specialising in open access (OA), research data management (RDM), open educational resources (OER) and virtual research environments (VRE). It collaborates closely with other KIM departments. This submission shall serve as a best practice example for the impact of OS on research libraries and, beyond that, the impact of research libraries on universities. To enhance and foster OS, the Team provides individual consultations, services and office hours for researchers. Here, it collaborates closely with other librarians like subject specialists and the Team University Publications. Along similar lines, the KIM offers institutional repositories for publications (KOPS) and research data (KonDATA). Beyond that, the Team provides solutions to host OA journals and analyses researchers’ VRE needs to decide on implementation options. In sum, the Team is the central OS contact point for the entire university, underlining the major role the library holds in making institutional impact. Furthermore, the Team had the leading role in creating the University of Konstanz’ OS Policy, one of the first ones passed by a German university. This policy stands out because it encompasses various OS domains. It demands, among other things, that text publications be made OA and that research data be managed according to relevant subject-specific standards. If permissible and reasonable, it demands that research data should be made publicly available at the earliest possible time. Along these lines, the policy has a large impact on how the library handles closed access books and subscription-based journals. As a consequence, OA is pursued wherever possible, leading to the highest OA quota of all German universities. In that sense, the Team is a crucial driving force of OS in the University of Konstanz, which ties in with the library’s major role of open research transformation. Beyond the University of Konstanz, the Team is involved in a range of national and international projects collaborating with other libraries. On a national level, they lead the project open.access-network which provides an information platform for researchers and librarians and connects the German-speaking OA community through events like bar camps. The project KOALA-AV supports libraries in establishing consortial solutions for financing Diamond OA publications. Moreover, the Team is involved in the federal state initiative for RDM in Baden-Württemberg (bwFDM). Here, the Team is in charge of forschungsdaten.info, the German-speaking countries’ leading RDM information platform, which will be offered in English within the next years. Internationally, the Team cooperates with librarians and other OS professionals from the European Reform University Alliance (ERUA) and the European University for Well-Being (EUniWell), establishing formats for best practice exchange, such as monthly OS Meet-Ups.
Interactive Image Data Flow Graphs#
Martin Schätz, Martin Schätz
Published 2022-10-17
Licensed CC-BY-4.0
The slides were presented during the Macro programming with ImageJ workshop (https://www.16mcm.cz/programme/#workshops) which was part of the 16th Multinational Congress on Microscopy. It is a collection and “reshuffle” of slides originally made by Robert Haase on topics from Image Analysis in general up to User-friendly GPU-accelerated bio-image analysis and CLIJ2.
Intravital microscopy contrasting agents for application - Database#
Michael Gerlach
Published 2024-06-19
Licensed CC-BY-4.0
This is a set of databases containing published use of substances which can be applied to rodents in order to contrast specific structures for optical intravital microscopy. The first dataset contains applied final dosages, calculated for 25g-mice, as well as the orignally published amounts, concentrations and application routes of agents directly applied into the target organism. The second dataset contains dosages and cell numbers for the external contrastation and subsequent application of cells into the target organism. Filtering possible for organ system and contrasted structure/cell type in both datasets, substance class and fluorescent detection windows can be filtered in the dataset for direct agent application. Source publications are listed by DOI.
Introduction to light-microscopy / Widefield microscopy#
Thomas Laurent
Published 2022-05-10
Licensed OTHER-AT
This is a short introduction to light-microscopy, illustrated with widefield microscopy.
It introduces :
upright and inverted widefield microscopes
the transmitted and fluorescent light-path
- contrasting methods (optical and at the sample level)
the molecular principle of fluorescence (Perrin-Jablonski)
objective, resolution and limitations of the method (diffraction, diffusion/scattering)
In addition to the PPT (with few animations), a lighter PDF version is provided for preview in Zenodo.
Illustrations are mostly extracted from the ThermoFisher Molecular Probes School of Fluorescence educator packet and from the course material from Micron Facility in Oxford.
As stated in the presentation, illustrations are copyrighted but can be reproduced provided the original attribution is conserved.
Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)#
Silke Tulok, Anja Nobst, Anett Jannasch, Tom Boissonnet, Gunar Fabig
Published 2024-06-28
Licensed CC-BY-4.0
This Key-Value pair template is used for the data documentation during imaging experiments and the later data annotation in OMERO. It is tailored for the usage and image acquisition at the slide scanning system Zeiss AxioScan 7 in the Core Facility Cellular Imaging (CFCI). It contains important metadata of the imaging experiment, which are not saved in the corresponding imaging files. All users of the Core Facility Cellular Imaging are trained to use that file to document their imaging parameters directly during the data acquisition with the possibility for a later upload to OMERO. Furthermore, there is a corresponding public example image used in the publication “Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users” and is available here: https://omero.med.tu-dresden.de/webclient/?show=image-33248 This template was developed by the CFCI staff during the setup and usage of the AxioScan 7 and is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015). With this template it is possible to create a csv-file, that can be used to annotate an image or dataset in OMERO using the annotation script (ome/omero-scripts). How to use:
fill the template sheet with your metadata select and copy the data range containing the Keys and Values open a new excel sheet and paste transpose in cell A1 Important: cell A1 contains always the name ‘dataset’ and cell A2 contains the exact name of the image/dataset, which should be annotated in OMERO save the new excel sheet in csv-file (comma separated values) format
An example can be seen in sheet 3 ‘csv_AxioScan’. Important note: The code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might be not able to decode by the annotation script. We encountered this issue with old Microsoft-Office versions (MS Office 2016). Note: By filling the values in the excel sheet, avoid the usage of comma as decimal delimiter. See cross reference: 10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO for light- and electron microscopy data within the research group of Prof. Mueller-Reichert 10.5281/zenodo.12546808 Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)
Key-Value pair template for annotation of datasets in OMERO (PERIKLES study)#
Anett Jannasch, Silke Tulok, Fuchs, Vanessa Aphaia Fiona, Tom Boissonnet, Christian Schmidt, Michele Bortolomeazzi, Gunar Fabig, Chukwuebuka Okafornta
Published 2024-06-26
Licensed CC-BY-4.0
This is a Key-Value pair template used for the annotation of datasets in OMERO. It is tailored for a research study (PERIKLES project) on the biocompatibility of newly designed biomaterials out of pericardial tissue for cardiovascular substitutes (https://doi.org/10.1063/5.0182672) conducted in the research department of Cardiac Surgery at the Faculty of Medicine Carl Gustav Carus at the Technische Universität Dresden . A corresponding public example dataset is used in the publication “Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users” and is available here (https://omero.med.tu-dresden.de/webclient/?show=dataset-1557). The template is based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) and it was developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- Sept 1th 2023. With this template it is possible to create a csv-file, that can be used to annotate a dataset in OMERO using the annotation script (ome/omero-scripts). How to use: select and copy the data range containing Keys and Values open a new excel sheet and paste transpose in column B1 type in A1 ‘dataset’ insert in A2 the exact name of the dataset, which should be annotated in OMERO save the new excel sheet in csv- (comma seperated values) file format
Example can be seen in sheet 1 ‘csv import’. Important note; the code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might not be able to decode by the annotation script. We encountered this issue with old Microsoft Office versions (e.g. MS Office 2016). Note: By filling the values in the excel sheet, avoid the usage of decimal delimiter. See cross reference: 10.5281/zenodo.12547566 Key-Value pair template for annotation of datasets in OMERO (light- and electron microscopy data within the research group of Prof. Mueller-Reichert) 10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)
Key-Value pair template for annotation of datasets in OMERO for light- and electron microscopy data within the research group of Prof. Müller-Reichert#
Fabig, Gunar, Jannasch, Anett, Okafornta, Chukwuebuka, Boissonnet, Tom, Schmidt, Christian, Bortolomeazzi, Michele, Fuchs, Vanessa Aphaia Fiona, Koeckert, Maria, Poddar, Aayush, Vogel, Martin, Schwarzbach, Hanna-Margareta, Vogelsang, Andy, Gerlach, Michael, Nobst, Anja, Müller-Reichert, Thomas, Tulok, Silke
Published 2024-06-26
Licensed CC-BY-4.0
This are a two Key-Value pair templates used for the annotation of datasets in OMERO. They are tailored for light- and electron microcopy data for all research projects of the research group of Prof. T. Mueller-Reichert. All members of the Core Facility Cellular Imaging agreed for using these templates to annotate data in OMERO. Furthermore, there are a corresponding public example datasets used in the publication “Setting up an institutional OMERO environment for bioimage data: perspectives from both facility staff and users” and are available here: https://omero.med.tu-dresden.de/webclient/?show=dataset-1552 –> for lattice-light sheet microscopy https://omero.med.tu-dresden.de/webclient/?show=dataset-1555–> for electron microscopy data That templates are based on the REMBI recommendations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8606015) and were developed during the PoL-Bio-Image Analysis Symposium in Dresden Aug 28th- Sept 1st in 2023 and further adapeted during the usage of OMERO. With every template it is possible to create a csv-file, that can be used to annotate a dataset in OMERO using the annotation script (ome/omero-scripts). How to use:
fill the template with metadata select and copy the data range containing the Keys and Values open a new excel sheet and paste transpose in cell A1 Important: cell A1 contains always the name ‘dataset’ and cell A2 contains the exact name of the dataset, which should be annotated in OMERO save the new excel sheet in csv-file (comma separated values) format
Examples can be seen in sheet 3 ‘csv_TOMO’ and sheet 5 csv_TEM’. Important note: The code has to be 8-Bit UCS transformation format (UTF-8) otherwise several characters (for example µ, %,°) might be not able to decode by the annotation script. We encountered this issue with old Microsoft-Office versions (MS Office 2016). Note: By filling the values in the excel sheet, avoid the usage of comma as decimal delimiter. See cross reference: 10.5281/zenodo.12546808 Key-Value pair template for annotation of datasets in OMERO (PERIKLES study) 10.5281/zenodo.12578084 Key-Value pair template for annotation in OMERO for light microscopy data acquired with AxioScan7 - Core Facility Cellular Imaging (CFCI)
Kollaboratives Arbeiten und Versionskontrolle mit Git#
Robert Haase
Published 2024-04-15
Licensed CC-BY-4.0
Gemeinsames Arbeiten im Internet stellt uns vor neue Herausforderungen: Wer hat eine Datei wann hochgeladen? Wer hat zum Inhalt beigetragen? Wie kann man Inhalte zusammenfuehren, wenn mehrere Mitarbeiter gleichzeitig Aenderungen gemacht haben? Das Versionskontrollwerkzeug git stellt eine umfassende Loesung fuer solche Fragen bereit. Die Onlineplatform github.com stellt nicht nur Softwareentwicklern weltweit eine git-getriebene Platform zur Verfuegung und erlaubt ihnen effektiv zusammen zu arbeiten. In diesem Workshop lernen wir:
Infuerung in FAIR-Prinzipien im Softwarecontext Arbeiten mit git: Pull-requests Aufloesen von Merge-Konflikten Automatisiertes Archivieren von Inhalten nach Zenodo.org Eigene Webseiten auf github.io publizieren
Tags: Research Data Management, FAIR-Principles, Git, Zenodo
Content type: Slides
LEO: Linking ELN with OMERO#
Escobar Diaz Guerrero, Rodrigo
Published 2024-05-08
Licensed CC-BY-4.0
First updates of LEO (Linking ELN with OMERO)
Large Language Models: An Introduction for Life Scientists#
Robert Haase
Published 2024-08-27
Licensed CC-BY-4.0
Large Language Models (LLMs) are changing the way how humans interact with computers. This has impact on all scientific fields by enabling new ways to achieve for example data analysis goals. In this talk we will go through an introduction to LLMs with respect to applications in the life sciences, focusing on bio-image analysis. We will see how to generate text and images using LLMs and how LLMs can extract information from reproducibly images through code-generation. We will go through selected prompt engineering techniques enabling scientists to tune the output of LLMs towards their scientific goal and how to do quality assurance in this context.
Large tiling confocal acquisition (rat brain)#
Julie Meystre
Published 2022-06-15
Licensed CC-BY-4.0
Name: Large tiling confocal acquisition (rat brain)
Microscope: Zeiss LSM700
Microscopy data type: 108 tiles, each with 62 z-slices and 2 channels : Channel 1: DAPI Channel 2: cck staining
File format: .lsm (16-bit)
Image size: 1024x1024x62 (Pixel size: 0.152 x 0.152 x 1 micron), 2 channels.
NOTE : Some tiles were annotated and used to train a StarDist3D model (https://doi.org/10.5281/zenodo.6645978 )
LauLauThom/MaskFromRois-Fiji: Masks from ROIs plugins for Fiji - initial release#
Laurent Thomas, Pierre Trehin
Published 2021-07-22
Licensed MIT
Fiji plugins for the creation of binary and semantic masks from ROIs in the RoiManager. Works with stacks too.
Installation in Fiji: activate the Rois from masks update site in Fiji.
See GitHub readme for the documentation.
Latest tested with Fiji 2.1.0/ImageJ 1.53j
Leitfaden zur digitalen Datensparsamkeit (mit Praxisbeispielen)#
Heber, Maximilian, Jakob, Moritz, Landwehr, Matthias, Leendertse, Jan, Müller, Maximilian, Schneider, Gabriel, von Suchodoletz, Dirk, Ulrich, Robert
Published 2024-06-03
Licensed CC-BY-4.0
Im Zuge der stetig wachsenden Brisanz des Forschungsdatenmanagements fallen immer größere Mengen an Forschungsdaten an. Diese an sich begrüßenswerte Entwicklung führt zu technischen und organisatorischen Herausforderungen nicht nur im Bereich der Speicherung von Forschungsdaten, sondern in allen Phasen des Forschungsdatenlebenszyklus. Der vorliegende Beitrag erläutert vor diesem Hintergrund mögliche Motivationen hinter digitaler Datensparsamkeit mit Blick auf organisatorische, technische und ethische Kriterien, Datenschutz und Nachhaltigkeit. Anschließend werden vor dem Hintergrund zentraler Herausforderungen Umsetzungsvorschläge für das Vorfeld sowie den Verlauf eines Forschungsvorhabens gemacht. Zudem werden grundlegende Empfehlungen zur digitalen Datensparsamkeit ausgesprochen. Eine kürzere Ausgabe des Leitfadens ist im Mai 2024 in der Zeitschrift o | bib erschienen: https://doi.org/10.5282/o-bib/6036 Diese Ausgabe enthält ein zusätzliches Kapitel (4.2) mit konkreten Praxisbeispielen. Dieser Artikel wurde ins Englische übersetzt: Heber, M., Jakob, M., Landwehr, M., Leendertse, J., Müller, M., Schneider, G., von Suchodoletz, D., & Ulrich, R. (2024). A Users’ Guide to Economical Digital Data Usage. Zenodo. https://doi.org/10.5281/zenodo.13752220
LimeSeg Test Datasets#
Sarah Machado, Vincent Mercier, Nicolas Chiaruttini
Published 2018-10-27
Licensed CC-BY-4.0
Image datasets from the publication : LimeSeg: A coarse-grained lipid membrane simulation for 3D image segmentation
Vesicles.tif: spinning-disc confocal images of giant unilamellar vesicles
HelaCell-FIBSEM.tif: a 3D Electron Microscopy (EM) dataset of nearly isotropic sections of a Hela cell, acquired with a focused ion beam scanning electron microscope (FIB-SEM). Sections are aligned with TrackEm2 (doi: ), without additional preprocessing.
DrosophilaEggChamber.tif: point scanning confocal images of a Drosophila egg chamber. Channel 1: cell nuclei stained with DAPI. Channel 2: cell membranes visualized with fused membrane proteins Nrg::GFP and Bsg::GFP.
Image metadata contains extra information including voxel sizes.
Linked (Open) Data for Microbial Population Biology#
Carsten Fortmann-Grote
Published 2024-03-12
Licensed CC-BY-4.0
Liver Micrometastases area quantification using QuPath and pixel classifier#
Laia Simó-Riudalbas, Romain Guiet, Olivier Burri, Julien Duc, Didier Trono
Published 2022-05-06
Licensed CC-BY-4.0
Sample: Mouse (NSG) liver slices with human colorectal cancer cells metastases, stained with Hematoxylin & Eosin.
Image Acquisition: Images were acquired on an Olympus VS120 Whole Slide Scanner, using a 20x objective (UPLSAPO, N.A. 0.75) and a color camera (Pike F505 Color) with an image pixel size of 0.345 microns.
Image Processing and Analysis: Obtained images were analyzed using the software QuPath [1] (version 0.3.2) using groovy scripts, making use of a pixel classifier to segment and measure cancer cell clusters.
Files :
Detailed_worflow.pdf : contains a detailed description of how pixel classifier was created
images_for_classifier_training.zip : contains all the vsi file obtained from the microscope and used for the training
project_for_classifier_training.zip : contains the QuPath project, with Training Image, annotations, classifiers and scripts for analysis
PythonCode.txt : code ran to transform output results from QuPath to final results
[1] Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5
Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm#
Romain Guiet, Olivier Burri, Mehmet Girgin, Matthias Lutolf
Published 2022-12-07
Licensed CC-BY-4.0
This imagej macro analyses the reporter intensity activity and expression domain in EPI aggregates and Gastruloids.
Metadata Annotation Workflow for OMERO with Tabbles#
Wendt Jens
Published 2023-09-04
Licensed CC-BY-4.0
Short presentation given at at PoL BioImage Analysis Symposium Dresden 2023
MicroSam-Talks#
Constantin Pape
Published 2024-05-23
Licensed CC-BY-4.0
Talks about Segment Anything for Microscopy: computational-cell-analytics/micro-sam. Currently contains slides for two talks:
Overview of Segment Anythign for Microscopy given at the SWISSBIAS online meeting in April 2024 Talk about vision foundation models and Segment Anything for Microscopy given at Human Technopole as part of the EMBO Deep Learning Course in May 2024
Tags: Image Segmentation, Bioimage Analysis, Deep Learning
Content type: Slides
Morphological analysis of neural cells with WEKA and SNT Fiji plugins#
Daniel Waiger
Published 2022-07-14
Licensed CC-BY-4.0
A simple workflow to detect Soma and neurite paths, from light microscopy datasets.
Using open-source tools for beginners.
Multi-Template-Matching for object-detection (slides)#
Laurent Thomas
Published 2022-05-16
Licensed CC-BY-4.0
This presentations describes Multi-Template-Matching, a novel method extending on template-matching for object-detection in images.
The project was part of the PhD project of Laurent Thomas between 2017 and 2020, under supervision of Jochen Gehrig. The project was hosted at ACQUIFER Imaging with collaboration of the medical university of Heidelberg, and part of the ImageInLife Horizon2020 ITN (PhD program).
Multiplexed histology of COVID-19 post-mortem lung samples - CONTROL CASE 1 FOV1#
Anna Pascual Reguant, Ronja Mothes, Helena Radbruch, Anja E. Hauser
Published 2022-12-16
Licensed CC-BY-4.0
Image-based data set of a post-mortem lung sample from a non-COVID-related pneumonia donor (CONTROL CASE 1, FOV1)
Each image shows the same field of view (FOV), sequentially stained with the depicted fluorescence-labelled antibodies, including surface proteins, intracellular proteins and transcription factors. Images contain 2024 x 2024 pixels and are generated using an inverted wide-field fluorescence microscope with a 20x objective, a lateral resolution of 325 nm and an axial resolution above 5 µm. Images have been normalized and intensities adjusted.
My Journey Through Bioimage Analysis Teaching Methods From Classroom to Cloud#
Elnaz Fazeli
Published 2024-02-19
Licensed CC-BY-4.0
In these slides I introducemy journey through teaching bioimage analysis courses in different formats, from in person courses to online material. I have an overview of different training formats and comparing these for different audiences.
Tags: Teaching
Content type: Slides
NFDI4BIOIMAGE#
Carsten Fortmann-Grote
Published 2024-04-22
Licensed CC-BY-4.0
This presentation was given at the 2nd MPG-NFDI Workshop on April 18th.
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis [conference talk: The Pelagic Imaging Consortium meets Helmholtz Imaging, 5.10.2023, Hamburg]#
Riccardo Massei
Licensed CC-BY-4.0
NFDI4BIOIMAGE is a consortium within the framework of the National Research Data Infrastructure (NFDI) in Germany. In this talk, the consortium and the contribution to the work programme by the Helmholtz Centre for Environmental Research (UFZ) in Leipzig are outlined.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and Bioimage Analysis#
Marcelo Zoccoler
Published 2024-08-07
Licensed CC-BY-4.0
Bioimaging refers to a collection of methods to visualize the internal structures and mechanisms of living organisms. The fundamental tool, the microscope, has enabled seminal discoveries like that of the cell as the smallest unit of life, and continues to expand our understanding of biological processes. Today, we can follow the interaction of single molecules within nanoseconds in a living cell, and the development of complete small organisms like fish and flies over several days starting from the fertilized egg. Each image pixel encodes multiple spatiotemporal and spectral dimensions, compounding the massive volume and complexity of bioimage data. Proper handling of this data is indispensable for analysis and its lack has become a growing hindrance for the many disciplines of the life and biomedical sciences relying on bioimaging. No single domain has the expertise to tackle this bottleneck alone. As a method-specific consortium, NFDI4BIOMAGE seeks to address these issues, enabling bioimaging data to be shared and re-used like they are acquired, i.e., independently of disciplinary boundaries. We will provide solutions for exploiting the full information content of bioimage data and enable new discoveries through sharing and re-analysis. Our RDM strategy is based on a robust needs analysis that derives not only from a community survey but also from over a decade of experience in German BioImaging, the German Society for Microscopy and Image Analysis. It considers the entire lifecycle of bioimaging data, from acquisition to archiving, including analysis and enabling re-use. A foundational element of this strategy is the definition of a common, cloud-compatible, and interoperable digital object that bundles binary images with their descriptive and provenance metadata. With members from plant biology to neuroscience, NFDI4BIOIMAGE will champion the standardization of bioimage data to create a framework that answers discipline-specific needs while ensuring communication and interoperability with data types and RDM systems across domains. Integration of bioimage data with, e.g., omics data as the basis for spatial omics, holds great promise for fields such as cancer medicine. Unlocking the full potential of bioimage data will rely on the development and broad availability of exceptional analysis tools and training sets. NFDI4BIOIMAGE will make these accessible and usable including cutting-edge AI-based methods in scalable cloud environments. NFDI4BIOIMAGE intersects with multiple NFDI consortia, most prominently with GHGA for linking image and genomics data and with DataPLANT on the definition of FAIR data objects. Last but not least, NFDI4BIOIMAGE is internationally well connected and represents the opportunity for German scientists to keep path with and have a voice in several international initiatives focusing on the FAIRification of bioimage data as one of the main challenges for the advancement of knowledge in the life and biomedical sciences.
NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne-Hackathon-2023, GitHub repository)#
Mohamed Abdrabbou, Mehrnaz Babaki, Tom Boissonnet, Michele Bortolomeazzi, Eik Dahms, Vanessa Fuchs, A. F. Moritz Hoevels, Niraj Kandpal, Christoph Möhl, Joshua A. Moore, Astrid Schauss, Andrea Schrader, Torsten Stöter, Julia Thönnißen, Monica Valencia-S., H. Lukas Weil, Jens Wendt, Peter Zentis
Licensed CC-BY-4.0
This repository documents the first NFDI4Bioimage - TA3-Hackathon - UoC-2023 (Cologne Hackathon), where topics like ‘Interoperability’, ‘REMBI / Mapping’, and ‘Neuroglancer (OMERO / zarr)’ were explored through collaborative discussions and workflow sessions, culminating in reports that bridge NFDI4Bioimage to DataPLANT. Funded by various DFG initiatives, this event emphasized documentation and use cases, contributing preparatory work for future interoperability projects at the 2nd de.NBI BioHackathon in Bielefeld.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Github Repository
NFDI4Bioimage Calendar 2024 October; original image#
Christian Jüngst, Peter Zentis
Published 2024-09-25
Licensed CC-BY-4.0
Raw microscopy image from the NFDI4Bioimage calendar October 2024
New Kid on the (NFDI) Block: NFDI4BIOIMAGE - A National Initiative for FAIR Data Management in Bioimaging and Bioimage Analysis#
Cornelia Wetzker
Published 2024-10-29
Licensed CC-BY-4.0
The poster introduces the consortium NFDI4BIOIMAGE with its central objectives, provides an overview of challenges in bioimage data handling, sharing and analysis and lists support options by the consortium through its data stewardship team. It is part of the work of the German consortium NFDI4BIOIMAGE funded by the Deutsche Forschungsgemeinschaft (DFG grant number NFDI 46/1, project number 501864659) and has been presented at the conference FDM@Campus held in Göttingen September 23-25, 2024.
Nextflow: Scalable and reproducible scientific workflows#
Floden Evan, Di Tommaso Paolo
Published 2020-12-17
Licensed CC-BY-4.0
Nextflow is an open-source workflow management system that prioritizes portability and reproducibility. It enables users to develop and seamlessly scale genomics workflows locally, on HPC clusters, or in major cloud providers’ infrastructures. Developed since 2014 and backed by a fast-growing community, the Nextflow ecosystem is made up of users and developers across academia, government and industry. It counts over 1M downloads and over 10K users worldwide.
Tags: Workflow Engine
Content type: Slide
Open Science, Sharing & Licensing#
Robert Haase
Published 2024-04-18
Licensed CC-BY-4.0
Wir tauchen ein in die Welt der Open Science und definieren Begriffe wie Open Source, Open Access und die FAIR-Prinzipien (Findable, Accessible, Interoperable and Reuasable). Wir diskutieren, wie diese Methoden der [wissenschaftlichen] Kommunikation und des Datenmanagements die Welt verändern und wie wir sie praktisch in unsere Arbeit integrieren können. Dabei spielen Aspekte wie Copyright und Lizenzierung eine wichtige Rolle.
Tags: Research Data Management, Open Access, FAIR-Principles, Licensing
Content type: Slides
Optimisation and Validation of a Swarm Intelligence based Segmentation Algorithm for low Contrast Positron Emission Tomography#
Robert Haase
Published 2014-04-01
Licensed CC-BY-4.0
In the field of radiooncological research, individualised therapy is one of the hot topics at the moment. As a key aspect biologically-adapted therapy is discussed. Therapy adaption based on biological parameters may include tomographic imaging to determine biological properties of the tumour. One often invoked imaging modality is positron emission tomography (PET) using the tracer [18F]-fluoromisonidazole (FMISO) for hypoxia imaging. Hypoxia imaging is of interest, because hypoxic tumours are known to be radiorestistant. Even further, patients with hypoxic tumours have worse prognosis compared to patients with normoxic tumours. Thus, hypoxia imaging appears promising for radiotherapy treatment adaption. For example, volumetric analysis of FMISO PET could deliver additional hypoxia target volumes, which may be irradiated with higher radiation doses to improve the therapeutic effect. However, limited contrast between target volume and background in FMISO PET images interferes image analysis.Established methods for target volume delineation in PET do not allow determination of reliable contours in FMISO PET. To tackle this aspect, this thesis focusses on an earlier developed swarm intelligence based segmentation algorithm for FMISO PET and rather, its optimisation and validation in a clinically relevant setting. In this setting, clinical FMISO PET images were used which were acquired as part of a clinical trial performed at the Clinic and Policlinic for Radiation Therapy and Radiooncology of the University Hospital Carl Gustav Carus Dresden. The segmentation algorithm was applied to these imaging data sets and optimised using a cross-validation approach incorporating reference contours from experienced observers who outlined FMISO PET positive volumes manually. Afterwards, the performance of the algorithm and the properties of the resulting contours were studied in more detail. The algorithm was shown to deliver contours which were similar to manually-created contours to a degree like manually-created contours were similar to each other. Thus, the application of the algorithm in clinical research is recommended to eliminate inter-observer-variabilities. Finally, it was shown that repeated FMISO PET imaging before and shortly after the beginning of combined radiochemotherapy lead to manually-created contours with significantly higher variations than the variations of automatically-created contours using the proposed algorithm. Increased contour similarity in subsequently acquired imaging data highlights the observer-independence of the algorithm. While several observers outline different volumes, in identical data sets as well as in subsequent imaging data sets, the algorithm outlines more stable volumes in both cases. Thus, increased contour reproducibility is reached by automation of the delineation process by the proposed algorithm.
Preprint: “Be Sustainable”, Recommendations for FAIR Resources in Life Sciences research: EOSC-Life’s Lessons#
Romain David, Arina Rybina, Jean-Marie Burel, Jean-Karim Heriche, Pauline Audergon, Jan-Willem Boiten, Frederik Coppens, Sara Crockett, Exter Katrina, Sven Fahrener, Maddalena Fratelli, Carole Goble, Philipp Gormanns, Tobias Grantner, Bjorn Gruning, Gurwitz, Kim Tamara, John Hancock, Henriette Harmse, Petr Holub, Nick Juty, Geoffrey Karnbach, Emma Karoune, Antje Keppler, Jessica Klemeier, Carla Lancelotti, Jean-Luc Legras, Lister, L. Allyson, Livio Longo, Dario, Rebecca Ludwig, Benedicte Madon, Marzia Massimi, Vera Matser, Rafaele Matteoni, Mayrhofer, Michaela Th., Christian Ohmann, Maria Panagiotopoulou, Helen Parkinson, Isabelle Perseil, Claudia Pfander, Roland Pieruschka, Michael Raess, Andreas Rauber, Richard, Audrey S., Paolo Romano, Antonio Rosato, Alex Sanchez-Pla, Susanna-Assunta Sansone, Ugis Sarkans, Beatriz Serrano-Solano, Jing Tang, Ziaurrehman Tanoli, Jonathan Tedds, Harald Wagener, Martin Weise, Westerhoff, Hans V., Rudolf Wittner, Jonathan Ewbank, Niklas Blomberg, Philip Gribbon
Published 2023-09-12
Licensed CC-BY-4.0
“Be SURE - Be SUstainable REcommendations”The main goals and challenges for the Life Science (LS) communities in the Open Science framework are to increase reuse and sustainability of data resources, software tools, and workflows, especially in large-scale data-driven research and computational analyses. Here, we present key findings, procedures, effective measures and recommendations for generating and establishing sustainable LS resources based on the collaborative, cross-disciplinary work done within the EOSC-Life (European Open Science Cloud for Life Sciences) consortium. Bringing together 13 European LS Research Infrastructures (RIs), it has laid the foundation for an open, digital space to support biological and medical research. Using lessons learned from 27 selected projects, we describe the organisational, technical, financial and legal/ethical challenges that represent the main barriers to sustainability in the life sciences. We show how EOSC-Life provides a model for sustainable FAIR data management, including solutions for sensitive- and industry-related resources, by means of cross-disciplinary training and best practices sharing. Finally, we illustrate how data harmonisation and collaborative work facilitate interoperability of tools, data, solutions and lead to a better understanding of concepts, semantics and functionalities in the life sciences.IN PRESS EMBO Journal: https://www.embopress.org/journal/14602075 AVAILABLE SOON at : https://doi.org/10.15252/embj.2023115008
QuPath: Open source software for analysing (awkward) images#
Peter Bankhead
Published 2020-12-16
Licensed CC-BY-4.0
Slides from the CZI/EOSS online meeting in December 2020.
Tags: Bioimage Analysis
Content type: Slide
RDF as a bridge to domain-platforms like OMERO, or There and back again.#
Josh Moore, Andra Waagmeester, Kristina Hettne, Katherine Wolstencroft, Susanne Kunis
Licensed CC-BY-4.0
In 2005, the first version of OMERO stored RDF natively. However, just a year after the 1.0 release of RDF, performance considerations led to the development of a more traditional SQL approach for OMERO. A binary protocol makes it possible to query and retrieve metadata but the resulting information cannot immediately be combined with other sources. This is the adventure of rediscovering the benefit of RDF triples as a – if not the – common exchange mechanism.
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis
Content type: Slides
RESEARCH DATA MANAGEMENT on Campus and in NFDI4BIOIMAGE#
Cornelia Wetzker, Michael Schlierf
Published 2024-08-29
Licensed CC-BY-4.0
The poster is part of the work of the German consortium NFDI4BIOIMAGE funded by the Deutsche Forschungsgemeinschaft (DFG grant number NFDI 46/1, project number 501864659).
Report on a pilot study: Implementation of OMERO for microscopy data management#
Silke Tulok, Gunar Fabig, Andy Vogelsang, Thomas Kugel, Thomas Müller-Reichert
Published 2023-11-10
Licensed CC-BY-4.0
The Core Facility Cellular Imaging (CFCI) at the Faculty of Medicine Carl Gustav Carus (TU Dresden) is currently running a pilot project for testing the use and handling of the OMERO software. This is done together with interested users of the imaging facility and a research group. Currently, we are pushing forward this pilot study on a small scale without any data steward. Our experiences argue so far for giving data management issues into the hands of dedicated personnel not fully involved in research projects. As funding agencies will ask for higher and higher standards for implementing FAIRdata principles in the future, this will be a releva
Research Data Management Seminar - Slides#
Della Chiesa, Stefano
Published 2022-05-18
Licensed CC-BY-4.0
This Research Data Management (RDM) Slides introduce to the multidisciplinary knowledge and competencies required to address policy compliance and research data management best practices throughout a project lifecycle, and beyond it.
Module 1 - Introduces the RDM giving its context in the Research Data Governance
Module 2 - Illustrates the most important RDM policies and principles
Module 3 - Provides the most relevant RDM knowledge bricks
Module 4 - Discuss the Data Management Plans (DMPs), examples, templates and guidance
Tags: Research Data Management
Content type: Slide
Research Data Managemet and how not to get overwhelmed with data#
Martin Schätz
Published 2023-09-23
Licensed CC-BY-4.0
Research data management and how not to get overwhelmed with data presentation is an overview of bioimage analysis with a focus on the basics for data management planning, FAIR principles, and how to practically organize folders and prepares naming convention. The presentation includes an overview of metadata, Creative Common licenses, and a sum up of electronic laboratory notebooks. The last two slides go through how all of that works in practice in open access core microscopy facility.
Round Table Workshop 1 - Sample Stabilization in intravital Imaging#
Michael Gerlach, Hans-Ulrich Fried, Christiane Peuckert
Published 2024-11-14
Licensed CC-BY-4.0
Notes from a round table workshop on the 4th Day of Intravital Microscopy in Leuven, Belgium. Contains hands-on tips, tricks and schemes to improve sample stability during various models of Intravital Miroscopy.
Round Table Workshop 2 - Correction of Drift and Movement#
Ishikawa-Ankerhold, Dr. Hellen, Max Nobis
Published 2024-11-14
Licensed CC-BY-4.0
Session 2 of a round table workshop. Features description of image processing methods useful in intravital imaging to compensate for the motion of living tissue.
SciAugment#
Martin Schätz
Published 2022-07-29
Licensed OTHER-OPEN
SciAugment v0.2.0 has pip installable version, channel-wise augmentation was added, and an option for all augmentations or no augmentation. Examples of how to use the tool are in README and in Google Colab notebooks. Practical examples of how to use results with YOLOv5 on scientific data can be found in the SciCount project.
SciAugment aims to provide an option to create an augmented image set with similar changes in data as the imaging sensor and technique would do.
Slides about FLUTE: a Python GUI for interactive phasor analysis of FLIM data#
Chiara Stringari
Published 2024-03-19
Licensed CC-BY-4.0
This presentation introduces the open source software to analyze FLIM data: FLUTE – (F)luorescence (L)ifetime (U)ltima(T)e (E)xplorer: a Python GUI for interactive phasor analysis of FLIM data The software is available on GitHub: LaboratoryOpticsBiosciences/FLUTE and it is published on Biological imaging Journal: Gottlieb, D., Asadipour, B., Kostina, P., Ung, T., & Stringari, C. (2023). FLUTE: A Python GUI for interactive phasor analysis of FLIM data. Biological Imaging, 1-22. doi:10.1017/S2633903X23000211 The lecture was part of the short talks on community developed FLIM-software at the German BioImaging workshop on FLIM in Munich.
So geschlossen wie nötig, so offen wie möglich - Datenschutz beim Umgang mit Forschungsdaten#
Pia Voigt
Published 2024-05-30
Licensed CC-BY-4.0
Der Umgang mit personenbezogenen Daten stellt Forschende oft vor rechtliche Herausforderungen: Unter welchen Bedingungen dürfen personenbezogene Daten verarbeitet werden? Welche Voraussetzungen müssen erfüllt sein und welche Strategien können angewendet werden, um Daten sicher speichern, verarbeiten, teilen und aufbewahren zu können? Mit Hilfe dieses Foliensatzes erhalten Sie Einblicke in datenschutzrechtliche Aspekte beim Umgang mit Ihren Forschungsdaten.
Tags: Research Data Management, Data Protection, FAIR-Principles
Content type: Slides
Stackview sliceplot example data#
Robert Haase
Published 2024-11-03
Licensed CC-BY-4.0
This is a dataset of PNG images of Bio-Image Data Science teaching slides. The png_umap.yml file contains a list of all images and a dimensionality reduced embedding (Uniform Manifold Approximation Projection, UMAP) made using OpenAI’s text-embedding-ada-002 model. A notebook for visualizing this data is published here: haesleinhuepf/stackview
Structuring of Data and Metadata in Bioimaging: Concepts and technical Solutions in the Context of Linked Data#
Sarah Weischer, Jens Wendt, Thomas Zobel
Published 2022-07-12
Licensed CC-BY-4.0
Provides an overview of contexts, frameworks, and models from the world of bioimage data as well as metadata. Visualizes the techniques for structuring this data as Linked Data. (Walkthrough Video: https://doi.org/10.5281/zenodo.7018928 )
Content:
Types of metadata
Data formats
Data Models Microscopy Data
Tools to edit/gather metadata
ISA Framework
FDO Framework
Ontology
RDF
JSON-LD
SPARQL
Knowledge Graph
Linked Data
Smart Data
...
Sustainable Data Stewardship#
Stefano Della Chiesa
Published 2024-03-25
Licensed CC-BY-4.0
These slides were presented at the 2. SaxFDM-Beratungsstammtisch and delve into the strategic integration of Research Data Management (RDM) within research organizations. The Leibniz IOER presented an insightful overview of RDM activities and approaches, emphasizing the criticality of embedding RDM strategically within research institutions. The presentation showcases some best practices in RDM implementation through practical examples, offering valuable insights for optimizing data stewardship processes.
Tags: Research Data Management, Data Stewardship
Content type: Slides
Test Dataset for Whole Slide Image Registration#
Romain Guiet, Nicolas Chiaruttini
Published 2021-04-12
Licensed CC-BY-4.0
Mouse duodenum fixed in 4% PFA overnight at 4°C, processed for paraffin infiltration using a standard histology procedure and cut at 4 microns were dewaxed, rehydrated, permeabilized with 0.5% Triton X-100 in PBS 1x and stained with Azide - Alexa Fluor 555 (Thermo Fisher) to detect EdU and DAPI for nuclei. The images were taken using a Leica DM5500 microscope with a 40X N.A.1 objective (black&white camera: DFC350FXR2, pixel dimension: 0.161 microns). Next, the slide was unmounted and stained using the fully automated Ventana Discovery xT autostainer (Roche Diagnostics, Rotkreuz, Switzerland). All steps were performed on automate with Ventana solutions. Sections were pretreated with heat using the CC1 solution under mild conditions. The primary rat anti BrDU (clone: BU1/75 (ICR1), Serotec, diluted 1:300) was incubated 1 hour at 37°C. After incubation with a donkey anti rat biotin diluted 1:200 (Jackson ImmunoResearch Laboratories), chromogenic revelation was performed with DabMap kit. The section was counterstained with Harris hematoxylin (J.T. Baker) before a second round of imaging on DM5500 PL Fluotar 40X N.A.1.0 oil (color camera: DFC 320 R2, pixel dimension: 0.1725 microns). Before acquisition, a white-balance as well as a shading correction is performed according to Leica LAS software wizard. The fluorescence and DAB images were converted in ome.tiff multiresolution file with the kheops Fiji Plugin.
Sampled prepared in the EPFL histology core facility by Nathalie Müller and Gian-Filippo Mancini.
Associated documents:
https://c4science.ch/w/bioimaging_and_optics_platform_biop/teaching/dab-intensity/
https://imagej.net/plugins/bdv/warpy/warpy
This document contains a full QuPath project with an example of registered image.
The Information Infrastructure for BioImage Data (I3D:bio) project to advance FAIR microscopy data management for the community#
Christian Schmidt, Michele Bortolomeazzi, Tom Boissonnet, Julia Dohle, Tobias Wernet, Janina Hanne, Roland Nitschke, Susanne Kunis, Karen Bernhardt, Stefanie Weidtkamp-Peters, Elisa Ferrando-May
Published 2024-03-04
Licensed CC-BY-4.0
Research data management (RDM) in microscopy and image analysis is a challenging task. Large files in proprietary formats, complex N-dimensional array structures, and various metadata models and formats can make image data handling inconvenient and difficult. For data organization, annotation, and sharing, researchers need solutions that fit everyday practice and comply with the FAIR (Findable, Accessible, Interoperable, Reusable) principles. International community-based efforts have begun creating open data models (OME), an open file format and translation library (OME-TIFF, Bio-Formats), data management software platforms, and microscopy metadata recommendations and annotation tools. Bringing these developments into practice requires support and training. Iterative feedback and tool improvement is needed to foster practical adoption by the scientific community. The Information Infrastructure for BioImage Data (I3D:bio) project works on guidelines, training resources, and practical assistance for FAIR microscopy RDM adoption with a focus on the management platform OMERO and metadata annotations.
The role of Helmholtz Centers in NFDI4BIOIMAGE - A national consortium enhancing FAIR data management for microscopy and bioimage analysis#
Riccardo Massei, Christian Schmidt, Michele Bortolomeazzi, Julia Thoennissen, Jan Bumberger, Timo Dickscheid, Jan-Philipp Mallm, Elisa Ferrando-May
Published 2024-06-06
Licensed CC-BY-4.0
Germany’s National Research Data Infrastructure (NFDI) aims to establish a sustained, cross-disciplinary research data management (RDM) infrastructure that enables researchers to handle FAIR (findable, accessible, interoperable, reusable) data. While FAIR principles have been adopted by funders, policymakers, and publishers, their practical implementation remains an ongoing effort. In the field of bio-imaging, harmonization of data formats, metadata ontologies, and open data repositories is necessary to achieve FAIR data. The NFDI4BIOIMAGE was established to address these issues and develop tools and best practices to facilitate FAIR microscopy and image analysis data in alignment with international community activities. The consortium operates through its Data Stewards team to provide expertise and direct support to help overcome RDM challenges. The three Helmholtz Centers in NFDI4BIOIMAGE aim to collaborate closely with other centers and initiatives, such as HMC, Helmholtz AI, and HIP. Here we present NFDI4BIOIMAGE’s work and its significance for research in Helmholtz and beyond
Thinking data management on different scales#
Susanne Kunis
Licensed CC-BY-4.0
Presentation given at PoL BioImage Analysis Symposium Dresden 2023
Tags: Research Data Management, Nfdi4Bioimage
Content type: Slides
Towards Preservation of Life Science Data with NFDI4BIOIMAGE#
Robert Haase
Published 2024-09-03
Licensed CC-BY-4.0
This talk will present the initiatives of the NFDI4BioImage consortium aimed at the long-term preservation of life science data. We will discuss our efforts to establish metadata standards, which are crucial for ensuring data reusability and integrity. The development of sustainable infrastructure is another key focus, enabling seamless data integration and analysis in the cloud. We will take a look at how we manage training materials and communicate with our community. Through these actions, NFDI4BioImage seeks to enable FAIR bioimage data management for German researchers, across disciplines and embedded in the international framework.
Towards Transparency and Knowledge Exchange in AI-assisted Data Analysis Code Generation#
Robert Haase
Published 2024-10-14
Licensed CC-BY-4.0
The integration of Large Language Models (LLMs) in scientific research presents both opportunities and challenges for life scientists. Key challenges include ensuring transparency in AI-generated content and facilitating efficient knowledge exchange among researchers. These issues arise from the in-transparent nature of AI-driven code generation and the informal sharing of AI insights, which may hinder reproducibility and collaboration. This paper introduces git-bob, an innovative AI-assistant designed to address these challenges by fostering an interactive and transparent collaboration platform within GitHub. By enabling seamless dialogue between humans and AI, git-bob ensures that AI contributions are transparent and reproducible. Moreover, it supports collaborative knowledge exchange, enhancing the interdisciplinary dialogue necessary for cutting-edge life sciences research. The open-source nature of git-bob further promotes accessibility and customization, positioning it as a vital tool in employing LLMs responsibly and effectively within scientific communities.
Train-the-Trainer Concept on Research Data Management#
Katarzyna Biernacka, Maik Bierwirth, Petra Buchholz, Dominika Dolzycka, Kerstin Helbig, Janna Neumann, Carolin Odebrecht, Cord Wiljes, Ulrike Wuttke
Published 2020-11-04
Licensed CC-BY-4.0
Within the project FDMentor, a German Train-the-Trainer Programme on Research Data Management (RDM) was developed and piloted in a series of workshops. The topics cover many aspects of research data management, such as data management plans and the publication of research data, as well as didactic units on learning concepts, workshop design and a range of didactic methods.
After the end of the project, the concept was supplemented and updated by members of the Sub-Working Group Training/Further Education (UAG Schulungen/Fortbildungen) of the DINI/nestor Working Group Research Data (DINI/nestor-AG Forschungsdaten). The newly published English version of the Train-the-Trainer Concept contains the translated concept, the materials and all methods of the Train-the-Trainer Programme. Furthermore, additional English references and materials complement this version.
Tags: Research Data Management
Content type: Book
Welcome to BioImage Town#
Josh Moore
Licensed CC-BY-4.0
Welcome at NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023
Tags: OMERO, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
Who you gonna call? - Data Stewards to the rescue#
Fuchs, Vanessa Aphaia Fiona, Jens Wendt, Maximilian Müller, Mohsen Ahmadi, Riccardo Massei, Cornelia Wetzker
Published 2024-03-01
Licensed CC-BY-4.0
The Data Steward Team of the NFDI4BIOIMAGE consortium presents themselves and the services (including the Helpdesk) that we offer.
Zeiss AxioZoom Stage Adapter#
Michael Gerlach
Published 2024-06-20
Licensed CC-BY-4.0
A 3D- printable microscope stage adapter for the reproducible accomodation of samples at a Zeiss AxioZoom stereomicroscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors.
Zeiss AxioZoom Stage Adapter - 12/6Well Plate#
Michael Gerlach
Published 2024-06-20
Licensed CC-BY-4.0
A 3D- printable microscope stage adapter for the reproducible accomodation of 6 or 12-well plates at a Zeiss AxioZoom microscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates a standard Greiner 6- or 12-well plate.
Zeiss AxioZoom Stage Adapter - EM block holder#
Michael Gerlach
Published 2024-06-20
Licensed CC-BY-4.0
A 3D- printable microscope stage adapter for the reproducible accomodation of EM Blocks at a Zeiss AxioZoom microscope.
4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates 70 standard resin EM blocks.
Zeiss AxioZoom Stage Adapter - Microscope slides#
Michael Gerlach
Published 2024-06-21
Licensed CC-BY-4.0
A 3D- printable microscope stage adapter for the reproducible accomodation of microscopic slides at a Zeiss AxioZoom microscope. 4 cylindrical anchors are fixed to the glass plate of the stage. The stage adapter is reversibly placed on these anchors and acommodates 4 standard glass slides.
[BINA CC] Scalable strategies for a next-generation of FAIR bioimaging#
Josh Moore
Published 2024-09-24
Licensed CC-BY-4.0
Presented at https://www.bioimagingnorthamerica.org/events/bina-2024-community-congress/
[CORDI 2023] Zarr: A Cloud-Optimized Storage for Interactive Access of Large Arrays#
Josh Moore
Licensed CC-BY-4.0
For decades, the sharing of large N-dimensional datasets has posed issues across multiple domains. Interactively accessing terabyte-scale data has previously required significant server resources to properly prepare cropped or down-sampled representations on the fly. Now, a cloud-native chunked format easing this burden has been adopted in the bioimaging domain for standardization. The format — Zarr — is potentially of interest for other consortia and sections of NFDI.
Tags: Research Data Management, Bioimage Analysis, Data Science
Content type: Poster
[Community Meeting 2024] Overview Team Image Data Analysis and Management#
Susanne Kunis, Thomas Zobel
Published 2024-03-08
Licensed CC-BY-4.0
Overview of Activities of the Team Image Data Analysis and Management of German BioImaging e.V.
[Community Meeting 2024] Supporting and financing RDM projects within GerBI#
Stefanie Weidtkamp-Peters, Josh Moore, Christian Schmidt, Roland Nitschke, Susanne Kunis, Thomas Zobel
Published 2024-03-28
Licensed CC-BY-4.0
Overview of GerBI RDM projects: why and how?
[ELMI 2024] AI’s Dirty Little Secret: Without#
FAIR Data, It’s Just Fancy Math
Josh Moore, Susanne Kunis
Published 2024-05-21
Licensed CC-BY-4.0
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/)
[ELMI 2024] AI’s Dirty Little Secret: Without FAIR Data, It’s Just Fancy Math#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Poster presented at the European Light Microscopy Initiative meeting in Liverpool (https://www.elmi2024.org/)
Tags: Research Data Management, FAIR-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Poster
[GBI EOE VII] Five (or ten) must-have items for making IT infrastructure for managing bioimage data#
Josh Moore
Published 2024-05-26
Licensed CC-BY-4.0
Presentation made to the GBI Image Data Management Working Group during the 7th Exchange of Experience in Uruguay.
[GBI EoE IX] NFDI4BIOIMAGE#
National Research Data Infrastructure for Microscopy and BioImage Analysis
Josh Moore
Published 2024-10-29
Licensed CC-BY-4.0
Presented at https://globalbioimaging.org/exchange-of-experience/exchange-of-experience-ix in Okazaki, Japan.
[I2K] Scalable strategies for a next-generation of FAIR bioimaging#
Josh Moore
Published 2024-10-25
Licensed CC-BY-4.0
or, “OME-Zarr: ‘even a talk on formats [can be] interesting’” Presented at https://events.humantechnopole.it/event/1/
[N4BI AHM] Welcome to BioImage Town#
Josh Moore
Published 2023-10-16
Licensed CC-BY-4.0
Keynote at the NFDI4BIOIMAGE All-Hands Meeting in Düsseldorf, Germany, October 16, 2023.
Tags: Research Data Management
Content type: Slides
[SWAT4HCLS 2023] NFDI4BIOIMAGE: Perspective for a national bioimage standard#
Josh Moore, Susanne Kunis
Licensed CC-BY-4.0
Poster presented at Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2023), Feb 13–16, 2023, Basel, Switzerland. NFDI4BIOIMAGE is a newly established German consortium dedicated to the FAIR representation of biological imaging data. A key deliverable is the definition of a semantically-compatible FAIR image object integrating RDF metadata with web-compatible storage of large n-dimensional binary data in OME-Zarr. We invite feedback from and collaboration with other endeavors during the soon-to-begin 5 year funding period.
Tags: Research Data Management, FAIR-Principles, Nfdi4Bioimage
Content type: Poster
[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure#
Christian Schmidt
Published 2024-04-10
Licensed CC-BY-4.0
Short Talk about the NFDI4BIOIMAGE consortium presented at the RDM in (Bio-)Medicine Information Event on April 10th, 2024, organized C³RDM & ZB MED.
[Workshop Material] Fit for OMERO - How imaging facilities and IT departments work together to enable RDM for bioimaging, October 16-17, 2024, Heidelberg#
Tom Boissonnet, Bettina Hagen, Susanne Kunis, Christian Schmidt, Stefanie Weidtkamp-Peters
Published 2024-11-18
Licensed CC-BY-4.0
Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging Description: Research data management (RDM) in bioimaging is challenging because of large file sizes, heterogeneous file formats and the variability of imaging methods. The image data management system OMERO (OME Remote Objects) allows for centralized and secure storage, organization, annotation, and interrogation of microscopy data by researchers. It is an internationally well-supported open-source software tool that has become one of the best-known image data management tools among bioimaging scientists. Nevertheless, the de novo setup of OMERO at an institute is a multi-stakeholder process that demands time, funds, organization and iterative implementation. In this workshop, participants learn how to begin setting up OMERO-based image data management at their institution. The topics include:
Stakeholder identification at the university / research institute Process management, time line expectations, and resources planning Learning about each other‘s perspectives on chances and challenges for RDM Funding opportunities and strategies for IT and imaging core facilities Hands-on: Setting up an OMERO server in a virtual machine environment
Target audience: This workshop was directed at universities and research institutions who consider or plan to implement OMERO, or are in an early phase of implementation. This workshop was intended for teams from IT departments and imaging facilities to participate together with one person from the IT department, and one person from the imaging core facility at the same institution. The trainers:
Prof. Dr. Stefanie Weidtkamp-Peters (Imaging Core Facility Head, Center for Advanced Imaging, Heinrich Heine University of Düsseldorf) Dr. Susanne Kunis (Software architect, OMERO administrator, metadata specialist, University of Osnabrück) Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich Heine University of Düsseldorf) Dr. Bettina Hagen (IT Administration and service specialist, Max Planck Institute for the Biology of Ageing, Cologne) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center (DKFZ), Heidelberg)
Time and place The format was a two-day, in-person workshop (October 16-17, 2024). Location: Heidelberg, Germany Workshop learning goals
Learn the steps to establish a local RDM environment fit for bioimaging data Create a network of IT experts and bioimaging specialists for bioimage RDM across institutions Establish a stakeholder process management for installing OMERO-based RDM Learn from each other, leverage different expertise Learn how to train users, establish sustainability strategies, and foster FAIR RDM for bioimaging at your institution
[Workshop] Bioimage data management and analysis with OMERO#
Riccardo Massei, Michele Bortolomeazzi, Christian Schmidt
Published 2024-05-13
Licensed CC-BY-4.0
Here we share the material used in a workshop held on May 13th, 2024, at the German Cancer Research Center in Heidelberg (on-premise) Description:Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. Image processing and analysis is a standard procedure to retrieve quantitative information from biological imaging. Due to the complex nature of bioimaging files that often come in proprietary formats, it can be challenging to organize, structure, and annotate bioimaging data throughout a project. Data often needs to be moved between collaboration partners, transformed into open formats, processed with a variety of software tools, and exported to smaller-sized images for presentation. The path from image acquisition to final publication figures with quantitative results must be documented and reproducible. In this workshop, participants learn how to use OMERO to organize their data and enrich the bioimage data with structured metadata annotations.We also focus on image analysis workflows in combination with OMERO based on the Fiji/ImageJ software and using Jupyter Notebooks. In the last part, we explore how OMERO can be used to create publication figures and prepare bioimage data for publication in a suitable repository such as the Bioimage Archive. Module 1 (9 am - 10.15 am): Basics of OMERO, data structuring and annotation Module 2 (10.45 am - 12.45 pm): OMERO and Fiji Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks Module 4 (4.15 pm - 6. pm): Publication-ready figures and data with OMERO The target group for this workshopThis workshop is directed at researchers at all career levels who plan to or have started to use OMERO for their microscopy research data management. We encourage the workshop participants to bring example data from their research to discuss suitable metadata annotation for their everyday practice. Prerequisites:Users should bring their laptops and have access to the internet through one of the following options:- eduroam- institutional WiFi- VPN connection to their institutional networks to access OMERO Who are the trainers? Dr. Riccardo Massei (Helmholtz-Center for Environmental Research, UFZ, Leipzig) - Data Steward for Bioimaging Data in NFDI4BIOIMAGE Dr. Michele Bortolomeazzi (DKFZ, Single cell Open Lab, bioimage data specialist, bioinformatician, staff scientist in the NFDI4BIOIMAGE project) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg, Project Coordinator of the NFDI4BIOIMAGE project)
[Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO#
Vanessa Fuchs, Fiona Aphaia, Christian Schmidt, Tom Boissonnet
Published 2024-05-06
Licensed CC-BY-4.0
Description Microscopy experiments generate information-rich, multi-dimensional data, allowing us to investigate biological processes at high spatial and temporal resolution. Image processing and analysis is a standard procedure to retrieve quantitative information from biological imaging. Due to the complex nature of bioimaging files that often come in proprietary formats, it can be challenging to organize, structure, and annotate bioimaging data throughout a project. Data often needs to be moved between collaboration partners, transformed into open formats, processed with a variety of software tools, and exported to smaller-sized images for presentation. The path from image acquisition to final publication figures with quantitative results must be documented and reproducible. In this workshop, participants learn how to use structured metadata annotations in the image data management platform OMERO (OME Remote Objects) to optimize their data handling. This strategy helps both with organizing data for easier processing and analysis and for the preparation of data publication in journal manuscripts and in public repositories such as the BioImage Archive. Participants learn the principles of leveraging object-oriented data organization in OMERO to enhance findability and usability of their data, also in collaborative settings. The integration of OMERO with image analysis tools, in particular ImageJ/Fiji, will be trained. Moreover, users learn about community-accepted metadata checklists (REMBI) to enrich the value of their data toward reproducibility and reusability. In this workshop, we will provide hands-on training and recommendations on:
Structured metadata annotation features in OMERO and how to use them Types of metadata in bioimaging: Technical metadata, sample metadata, analysis metadata The use of ontologies and terminologies for metadata annotation REMBI, the recommended metadata for biological images Metadata-assisted image analysis streamlining Tools for metadata annotation in OMERO
The target group for this workshop This workshop is directed at researchers at all career levels who have started using OMERO for their microscopy research data management. We encourage the workshop participants to bring example data from their research to discuss suitable metadata annotation for their everyday practice. Who are the trainers (see trainer description below for more details)
Dr. Vanessa Fuchs (NFDI4BIOIMAGE Data Steward, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) Dr. Tom Boissonnet (OMERO admin and image metadata specialist, Center for Advanced Imaging, Heinrich-Heine University of Düsseldorf) Dr. Christian Schmidt (Science Manager for Research Data Management in Bioimaging, German Cancer Research Center, Heidelberg)
Material Description Published here are the presentation slides that were used for input from the trainers during the different sessions of the programme. Additionally, a Fiji Macro is published that depends on the OMERO Extensions Plugin by Pouchin et al, 2022, F100Research, https://doi.org/10.12688/f1000research.110385.2 Programme Overview Day 1 - April 29th, 2024 09.00 a.m. to 10.00 a.m.: Session 1 - Welcome and Introduction 10.00 a.m. to 10.30 a.m.: Session 2 - Introduction to the FAIR principles & data annotation 10:30 a.m. to 10:45 a.m.: Coffee break 10.45 a.m. to 12.00 a.m.: Session 3 - Data structure (datasets in OMERO) and organization with Tags 12.00 a.m. to 1.00 p.m.: Lunch Break 1.00 p.m. to 2.00 p.m.: Session 4 - REMBI, Key-Value pair annotations in bioimaging 2:00 p.m. to 2.30 p.m.: Session 5 - Ontologies for Key-Value Pairs in OMERO 2:30 p.m. to 2:45 p.m. Coffee break 2.45 p.m. to 3.45 p.m.: Wrap-up, discussion, outlook on day 2 Day 2 - April 30th, 2024 09.00 a.m. to 09.30 a.m.: Arrival and Start into day 2 09.30 a.m. to 11.30 a.m.: Session 6 - Hands-on : REMBI-based Key-Value Pair annotation in OMERO 11.30 a.m. to 12.30 a.m.: Lunch Break 12.30 a.m. to 1.15 p.m.: Session 7 - OMERO and OMERO.plugins 1.15 p.m. to 2.00 p.m.: Session 8 - Loading OMERO-hosted data into Fiji 2.00 p.m. to 2.15 p.m.: Coffee break 2.15 p.m. to 3.00 p.m.: Discussion, Outlook
ilastik: interactive machine learning for (bio)image analysis#
Anna Kreshuk, Dominik Kutra
Licensed CC-BY-4.0
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
martinschatz-cz/SciCount: v1.0.0 with reusable example notebooks#
Martin Schätz, Lukáš Mrazík, Karolina Máhlerova
Published 2022-08-02
Licensed OTHER-OPEN
The first version contains an example of augmentation of scientific data and object detection with YOLO_v5 on colony counting (2 classes), object counting in blood smears (can be used as semisupervised learning for faster annotation), and wildlife detection from night records with a camera trap.
The project is available on GitHub.
quantixed/TheDigitalCell: First complete code set#
Stephen Royle
Published 2019-04-17
Licensed GPL-3.0
First complete code set for The Digital Cell book.
Tags: Bioimage Analysis
Content type: Code
https://zenodo.org/records/2643411
https://doi.org/10.5281/zenodo.2643411