Collection (79)#
A biologist’s guide to planning and performing quantitative bioimaging experiments#
Rebecca A. Senft, Barbara Diaz-Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L. Evans III, Kevin W. Eliceiri, Beth A. Cimini
Licensed BSD-3-CLAUSE
Content type: Collection, Publication
Annotated high-throughput microscopy image sets for validation#
Vebjorn Ljosa, Katherine L Sokolnicki, Anne E Carpenter
Broad Bioimage Benchmark Collection (BBBC)
Content type: Collection, Data
Bio Image Analysis Lecture 2020#
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/watch?v=e-2DbkUwKk4&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U
Bio-image Analysis ICOB 2023#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Kioto and Taipei 23/24#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio-image Analysis Workshop Taipei#
Tags: Bioimage Analysis
Content type: Workshop, Collection
Bio.tools database#
Licensed CC-BY-4.0
Tags: Bioinformatics
Content type: Collection
BioImage Archive AI Gallery#
Licensed CC0-1.0
Tags: Bioimage Analysis, Deep Learning
Content type: Collection, Data
BioImage Archive Visual Gallery#
Licensed CC0-1.0
Tags: Bioimage Analysis
Content type: Collection, Data
https://www.ebi.ac.uk/bioimage-archive/galleries/visualisation.html
BioImage Archive Volume EM Gallery#
Licensed CC0-1.0
Tags: Bioimage Analysis
Content type: Collection, Data
BioImage Informatics Index Training Materials#
Licensed ODC-BY-1.0
Tags: Bioimage Analysis
Content type: Collection
Bioimage Archive#
Content type: Collection, Data, Publication
https://www.ebi.ac.uk/bioimage-archive/
https://www.sciencedirect.com/science/article/abs/pii/S0022283622000791
Bioimage Model Zoo#
Licensed UNKNOWN
Tags: Bioimage Analysis, Artificial Intelligence
Content type: Collection
Bioimage analysis with Napari#
Fabrizio Musacchio
Licensed CC-BY-ND-SA-4.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection
https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/
COBA: Center for Open Bioimage Analysis YouTube Channel#
Tags: Bioimage Analysis
Content type: Collection, Video
CZI: Open Science Program Collection#
Content type: Collection
Cell Tracking Challenge - 2D Datasets#
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Collection, Data
Cell Tracking Challenge - 3D Datasets#
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Collection, Data
CellTrackColab#
Guillaume Jacquemet
Licensed MIT
Content type: Notebook, Collection
Center for Microscopy and Image Analysis How-to Guides#
Content type: Collection
Chris Halvin YouTube channel#
Licensed UNKNOWN
Tags: Napari, Python, Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/@chrishavlin
https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1
Community-developed checklists for publishing images and image analyses#
Beth Cimini et al.
Licensed BSD LICENSE
This book is a companion to the Nature Methods publication Community-developed checklists for publishing images and image analyses. In this paper, members of QUAREP-LiMi have proposed 3 sets of standards for publishing image figures and image analysis - minimal requirements, recommended additions, and ideal comprehensive goals. By following this guidance, we hope to remove some of the stress non-experts may face in determining what they need to do, and we also believe that researchers will find their science more interpretable and more reproducible.
Tags: Bioimage Analysis, Research Data Management
Content type: Notebook, Collection
https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html
DL4MicEverywhere#
Iván Hidalgo, et al.
Licensed CC-BY-4.0
Content type: Notebook, Collection
Data life cycle#
ELIXIR (2021) Research Data Management Kit
Licensed CC-BY-4.0
In this section, information is organised according to the stages of the research data life cycle.
Tags: Data Life Cycle, Research Data Management
Content type: Collection, Website, Online Tutorial
DataPLANT knowledge base#
Published 2022-12-14
Licensed CC-BY-4.0
Explore fundamental topics on research data management (RDM), how DataPLANT implements these aspects to support plant researchers with RDM tools and services, read guides and manuals or search for some teaching materials.
Tags: Research Data Management, Training, Dataplant
Content type: Collection
https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html
DigitalSreeni YouTube Channel#
Sreeni Bhattiprolu
A collection tutorial videos for using Python in general and for processing images using Python, machine learning and deep learning
Tags: Python
Content type: Collection, Video
EMBL-EBI material collection#
EMBL-EBI
Licensed CC0 (MOSTLY, BUT CAN DIFFER DEPENDING ON RESOURCE)
Online tutorial and webinar library, designed and delivered by EMBL-EBI experts
Tags: Bioinformatics, Training
Content type: Collection
https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=
Elastix tutorial#
Marvin Albert
Licensed BSD LICENSE
Tutorial material for teaching the basics of (itk-)elastix for image registration in microscopy images.
Tags: Image Registration, Itk, Elastix
Content type: Notebook, Collection
Euro-BioImaging Communication YouTube Channel#
Content type: Collection, Video
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
FAIR BioImage Data#
Licensed CC-BY-4.0
Tags: Research Data Management, Fair, Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/watch?v=8zd4KTy-oYI&list=PLW-oxncaXRqU4XqduJzwFHvWLF06PvdVm
FAIR Priciples#
Licensed CC-BY-4.0
In 2016, the ‘FAIR Guiding Principles for scientific data management and stewardship’ were published in Scientific Data. The authors intended to provide guidelines to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets.
Tags: FAIR-Principles, Data Stewardship, Research Data Management
Content type: Collection
Fiji Is Just ImageJ Tutorials#
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/playlist?list=PL5Edc1v41fyCLFZbBCLo41zFO-_cXBfAb
Finding and using publicly available data#
Anna Swan
Published 2024-01-01
Licensed CC-BY-4.0
Sharing knowledge and data in the life sciences allows us to learn from each other and built on what others have discovered. This collection of online courses brings together a variety of training, covering topics such as biocuration, open data, restricted access data and finding publicly available data, to help you discover and make the most of publicly available data in the life sciences.
Tags: Open Science, Teaching, Sharing
Content type: Collection, Tutorial, Videos
https://www.ebi.ac.uk/training/online/courses/finding-using-public-data/
Forschungsdaten.info#
Licensed PUBLIC DOMAIN
Research Data Management Information Portal in German
Tags: Research Data Management
Content type: Collection
Forschungsdaten.org#
Licensed CC-BY-4.0
Research Data Management Wiki in German
Tags: Research Data Management
Content type: Collection
Galaxy Training#
Published None
Licensed CC-BY-4.0
Collection of tutorials developed and maintained by the worldwide Galaxy community.
Tags: Bioimage Analysis, Data Analysis
Content type: Collection, Tutorial
GerBI Teaching Resources Link List#
Licensed UNKNOWN
List of training materials by the German BioImaging community provided by facilities, the scientific community, and companies.
Content type: Collection
Glencoe Software Webinars#
Chris Allan, Emil Rozbicki
Licensed UNKNOWN
Example Workflows / usage of the Glencoe Software.
Tags: OMERO, Training
Content type: Videos, Tutorial, Collection
Global BioImaging Training Database#
Tags: Bioimage Analysis
Content type: Collection, Event
Global BioImaging YouTube channel#
Content type: Collection, Video
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
I3D bio – Information Infrastructure for BioImage Data - Bioimage Metadata#
Christian Schmidt
Licensed UNKNOWN
A Microscopy Research Data Management Resource.
Tags: Metadata, I3Dbio, Research Data Management, Bioimage Data
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/
I3D:bio list of online training material#
Licensed UNKNOWN
List of links to training materials by the I3D:bio community.
Tags: Research Data Management
Content type: Collection
https://gerbi-gmb.de/i3dbio/i3dbio-teaching/train-mat/bioimagelist/
Ibiology. Bioimage Analysis Course. The Life Cycle of an Image Data Set#
Licensed CC BY-NC-ND 3.0 DEED
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/
Image Data Resources#
Content type: Collection, Data, Publication
Image Processing with Python#
Jacob Deppen, Kimberly Meechan, David Palmquist, Ulf Schiller, Robert Turner, Marianne Corvellec, Toby Hodges, et al.
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis
Content type: Collection
Imaris Tutorials#
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Collection, Video
Key-Value pairs scripts#
Licensed UNKNOWN
The key-value pairs are annotations in OMERO useful to describe thoroughly the data and can be added & edited via the OMERO.web interface.
Tags: OMERO
Content type: Documentation, Collection
Melbourne Advanced Microscopy Facility#
Collection of tutorial videos for Fiji users
Tags: Bioimage Analysis
Content type: Collection, Video
Metrics Reloaded - A framework for trustworthy image analysis validation#
Licensed UNKNOWN
The mission of Metrics Reloaded is to guide researchers in the selection of appropriate performance metrics for biomedical image analysis problems, as well as provide a comprehensive online resource for metric-related information and pitfalls
Tags: Bioimage Analysis, Image Segmentation, Machine Learning
Content type: Website, Collection
MicroscopyDB#
Licensed ALL RIGHTS RESERVED
Content type: Collection
NEUBIAS YouTube Channel#
A collection of bio-image analysis webinars where commonly authors of open-source bio-image analysis software explain how to use their tools.
Tags: Neubias
Content type: Collection, Video
NextFlow core#
nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow
Tags: Python
Content type: Collection
OME Event Database#
Tags: OMERO, Research Data Management
Content type: Collection, Event
OMERO Guide#
Licensed BSD-2-CLAUSE
Tags: OMERO
Content type: Collection
Omero Deployment examples#
Licensed BSD-2-CLAUSE
Tags: OMERO
Content type: Collection
Open Micoscropy Environment (OME) Youtube Channel#
Published None
Licensed CC-BY-4.0
OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data
Tags: Open Source Software, Microscopy Image Analysis, Bioimage Data
Content type: Video, Collection
Open Microscopy Environment YouTube channel#
YouTube channel collecting videos and webinar recordings about the Open Microscopy Environment (OME), the Next Generation File Format OME-NGFF, the Image Data Resource (IDR), the Omero platform and Omero plugins.
Tags: OMERO
Content type: Collection, Video
Python for Microscopists#
Sreenivas Bhattiprolu
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Notebook, Collection
QuPath for Python programmers#
Alan O’Callaghan, Léo Leplat
Published 2024-10-23
Licensed UNKNOWN
These are the notebooks and associated files for the i2k 2024 QuPath for Python programmers workshop.
Tags: Python, Notebooks, Open Source Software, Bioimage Analysis
Content type: Github Repository, Notebook, Collection
RDM4Mic Presentations#
Licensed CC-BY-4.0
Tags: Research Data Management
Content type: Collection
RDM4mic#
Licensed UNKNOWN
Tags: Research Data Management, OMERO
Content type: Collection, Video
RDMBites BioImage metadata#
Content type: Collection, Video
https://www.youtube.com/watch?v=aRHNHk07t3Q&list=PLyCNTVs-UBvuJF7WausQ5q7v7pI1vEpI1
RDMKit Training Resources#
Licensed CC-BY-4.0
Tags: Research Data Management
Content type: Collection
REMBI Overview#
Licensed CC0-1.0
Recommended Metadata for Biological Images (REMBI) provides guidelines for metadata for biological images to enable the FAIR sharing of scientific data.
Tags: FAIR-Principles, Metadata, Image Data Management, Research Data Management, Bioimage Data
Content type: Collection
Reporting and reproducibility in microscopy#
Published 2021-12-03
Licensed UNKNOWN
This Focus issue features a series of papers offering guidelines and tools for improving the tracking and reporting of microscopy metadata with an emphasis on reproducibility and data re-use.
Tags: Reproducibility, Metadata, Bioimage Data
Content type: Collection
SWC/GCNU Software Skills#
Licensed CC-BY-4.0
Computational skills training at the UCL Sainsbury Wellcome Centre and Gatsby Computational Neuroscience Unit, delivered by members of the Neuroinformatics Unit.
Tags: Training
Content type: Collection, Online Course, Videos, Tutorial
TESS Event database#
Tags: Bioinformatics
Content type: Collection, Event
TESS training materials#
Licensed UNKNOWN
Tags: Bioinformatics
Content type: Collection
Tess Search for Data Life Cycle#
Licensed UNKNOWN
Tags: Data Life Cycle, Research Data Management
Content type: Collection
https://tess.elixir-europe.org/search?q=data+life+cycle#materials
Upcoming Image Analysis Events#
Curtis Rueden, Albane de la Villegeorges, Simon F. Nørrelykke, Romain Guiet, Olivier Burri, et al.
Licensed UNKNOWN
Tags: Bioimage Analysis, Microscopy Image Analysis
Content type: Collection, Event, Forum Post, Workshop
https://forum.image.sc/t/upcoming-image-analysis-events/60018/67
What is Open Data?#
Daniel Dietrich, Jonathan Gray, Tim McNamara, Antti Poikola, Rufus Pollock, et al.
Licensed CC-BY-4.0
This handbook is about open data but what exactly is it? In particular what makes open data open, and what sorts of data are we talking about?
Tags: Open Science
Content type: Collection
WorkflowHub#
Stian Soiland-Reyes, Finn Bacall, Bert Droesbeke, Alan R Williams, Johan Gustafsson, et al.
Licensed BSD-3-CLAUSE
A registry for describing, sharing and publishing scientific computational workflows.
Tags: Bioinformatics, Workflow, Workflow Engine, Python, R
Content type: Collection
Workshop-June2024-Madrid#
Licensed MIT
Tags: Bioimage Analysis
Content type: Workshop, Collection
ZEN & Python workshop#
Licensed GPL-3.0
Tags: Python, Napari, Bioimage Analysis
Content type: Collection, Notebook
ZeroCostDL4Mic: exploiting Google Colab to develop a free and open-source toolbox for Deep-Learning in microscopy#
Lucas von Chamier, Romain F. Laine, Johanna Jukkala, Christoph Spahn, Daniel Krentzel, Elias Nehme, Martina Lerche, Sara Hernández-pérez, Pieta Mattila, Eleni Karinou, Séamus Holden, Ahmet Can Solak, Alexander Krull, Tim-Oliver Buchholz, Martin L Jones, Loic Alain Royer, Christophe Leterrier, Yoav Shechtman, Florian Jug, Mike Heilemann, Guillaume Jacquemet, Ricardo Henriques
Licensed MIT
Content type: Notebook, Collection
arivis Vision4D Tutorials#
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/playlist?list=PLRc9dt9lEZh_SVRC4G5moOvgHuvjPwmv0
microlist#
Licensed ALL RIGHTS RESERVED
A searchable database of resources for light and electron microscopists
Content type: Collection