Bioimage analysis (133)#
2020 BioImage Analysis Survey: Community experiences and needs for the future#
[‘Nasim Jamali’, ‘Ellen T. A. Dobson’, ‘Kevin W. Eliceiri’, ‘Anne E. Carpenter’, ‘Beth A. Cimini’]
Published 2021
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication
2022 MIC Workshop on Bioimage processing with Python#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis
Content type: Notebook
A Fiji Scripting Tutorial#
[‘Albert Cardona’]
Licensed CC0-1.0
Tags: Imagej, Bioimage Analysis
Content type: Notebook
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’]
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.
Tags: Bioimage Analysis, Flim
Content type: Slides
A Hitchhiker’s guide through the bio-image analysis software universe#
[‘Robert Haase’, ‘Elnaz Fazeli’, ‘David Legland’, ‘Michael Doube’, ‘Siân Culley’, ‘Ilya Belevich’, ‘Eija Jokitalo’, ‘Martin Schorb’, ‘Anna Klemm’, ‘Christian Tischer’]
Licensed CC-BY-4.0
This article gives an overview about commonly used bioimage analysis software and which aspects to consider when choosing a software for a specific project.
Tags: Bioimage Analysis
Content type: Publication
https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.14451
Adding a Workflow to BIAFLOWS#
[‘Sébastien Tosi’, ‘Volker Baecker’, ‘Benjamin Pavie’]
Licensed BSD-2-CLAUSE
Tags: Neubias, Bioimage Analysis
Content type: Slide
Annotating 3D images in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/30/annotating-3d-images-in-napari/
BIDS-lecture-2024#
[‘Robert Haase’]
Licensed CC-BY-4.0
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: Github Repository
Basics of Image Processing and Analysis#
[‘Kota Miura’]
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Book
BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data#
[‘Christian Tischer’, ‘Ashis Ravindran’, ‘Sabine Reither’, ‘Nicolas Chiaruttini’, ‘Rainer Pepperkok’, ‘Nils Norlin’]
Licensed CC-BY-4.0
Tags: Research Data Management, Bioimage Analysis
Content type: Publication
Bio Image Analysis#
[‘Christian Tischer’]
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Slide
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-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
Bio-image analysis, biostatistics, programming and machine learning for computational biology#
[‘Anna Poetsch’, ‘Biotec Dresden’, ‘Marcelo Leomil Zoccoler’, ‘Johannes Richard Müller’, ‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Napari
Content type: Notebook
BioImage Analysis Notebooks#
[‘Robert Haase et al.’]
Licensed [‘CC-BY-4.0’, ‘BSD-3-CLAUSE’]
Tags: Python, Bioimage Analysis
Content type: Book, Notebook
https://haesleinhuepf.github.io/BioImageAnalysisNotebooks/intro.html
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 Data Analysis#
[‘Kota Miura’]
Licensed ALL RIGHTS RESERVED
Tags: Neubias, Bioimage Analysis
Content type: Book
https://analyticalscience.wiley.com/do/10.1002/was.00050003/full/bioimagedataanalysis.pdf
BioImage Informatics Index Training Materials#
Licensed ODC-BY-1.0
Tags: Bioimage Analysis
Content type: Collection
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/
Bridging Imaging Users to Imaging Analysis - A community survey#
[‘Suganya Sivagurunathan’, ‘Stefania Marcotti’, ‘Carl J Nelson’, ‘Martin L Jones’, ‘David J Barry’, ‘Thomas J A Slater’, ‘Kevin W Eliceiri’, ‘Beth A Cimini’]
Published 2023
Licensed BSD-3-CLAUSE
Tags: Bioimage Analysis
Content type: Publication, Preprint
Bring your own data workshops#
Tags: Bioimage Analysis, Research Data Management
Content type: Workshop
Building a Bioimage Analysis Workflow using Deep Learning#
[‘Estibaliz Gómez-de-Mariscal']
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
CARE/Stardist tutorials for EMBO Practical Course — Computational optical biology 2022#
[‘Martin Weigert’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
CLIJ: GPU-accelerated image processing for everyone#
[‘Robert Haase’, ‘Loic Royer’, ‘et al.’]
Published 2020
Licensed ALL RIGHTS RESERVED
CLIJ is a collection of image processing functions that use graphics processing units for accelerated processing.
Tags: Imagej, Bioimage Analysis
Content type: Publication
COBA: Center for Open Bioimage Analysis YouTube Channel#
Tags: Bioimage Analysis
Content type: Collection, Video
CSBDeep and StarDist @ I2K 2020#
[‘Martin Weigert’, ‘Uwe Schmidt’]
Licensed UNKNOWN
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
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
CellProfiler Introduction#
[‘Anna Klemm’]
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Slide
CellProfiler Practical NeuBIAS Lisbon 2017#
[‘Carolina Wählby’, ‘Maxime Bombrun’, ‘Christian Tischer’]
Licensed UNKNOWN
Tags: Neubias, Cellprofiler, Bioimage Analysis
Content type: Tutorial
CellProfiler tutorials#
Licensed BSD-3-CLAUSE
CellProfiler tutorials and guided exercises about translocation, segmentation, pixel-based classification and quality control
Tags: Cellprofiler, Bioimage Analysis
Content type: Notebook
Challenges and opportunities for bioimage analysis core-facilities#
[‘Johannes Richard Soltwedel’, ‘Robert Haase’]
Licensed CC-BY-4.0
This article outlines common reasons for founding bioimage analysis core-facilities, services they can provide to fulfill certain need and conflicts of interest that arise from these services.
Tags: Bioimage Analysis, Research Data Management
Content type: Publication
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
Collection of teaching material for deep learning for (biomedical) image analysis#
[‘Constantin Pape’]
Licensed MIT
Tags: Artificial Intelligence, Bioimage Analysis
Community-developed checklists for publishing images and image analyses#
[‘Christopher Schmied’, ‘Michael S Nelson’, ‘Sergiy Avilov’, ‘Gert-Jan Bakker’, ‘Cristina Bertocchi’, ‘Johanna Bischof’, ‘Ulrike Boehm’, ‘Jan Brocher’, ‘Mariana T Carvalho’, ‘Catalin Chiritescu’, ‘Jana Christopher’, ‘Beth A Cimini’, ‘Eduardo Conde-Sousa’, ‘Michael Ebner’, ‘Rupert Ecker’, ‘Kevin Eliceiri’, ‘Julia Fernandez-Rodriguez’, ‘Nathalie Gaudreault’, ‘Laurent Gelman’, ‘David Grunwald’, ‘Tingting Gu’, ‘Nadia Halidi’, ‘Mathias Hammer’, ‘Matthew Hartley’, ‘Marie Held’, ‘Florian Jug’, ‘Varun Kapoor’, ‘Ayse Aslihan Koksoy’, ‘Judith Lacoste’, ‘Sylvia Le Dévédec’, ‘Sylvie Le Guyader’, ‘Penghuan Liu’, ‘Gabriel G Martins’, ‘Aastha Mathur’, ‘Kota Miura’, ‘Paula Montero Llopis’, ‘Roland Nitschke’, ‘Alison North’, ‘Adam C Parslow’, ‘Alex Payne-Dwyer’, ‘Laure Plantard’, ‘Rizwan Ali’, ‘Britta Schroth-Diez’, ‘Lucas Schütz’, ‘Ryan T Scott’, ‘Arne Seitz’, ‘Olaf Selchow’, ‘Ved P Sharma’, ‘Martin Spitaler’, ‘Sathya Srinivasan’, ‘Caterina Strambio-De-Castillia’, ‘Douglas Taatjes’, ‘Christian Tischer’, ‘Helena Klara Jambor’]
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Publication
Course on Deep Learning for imaging using PyTorch#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Notebook
DEEP NAPARI : Napari as a tool for deep learning project management#
[‘Herearii Metuarea’, ‘David Rousseau’, ‘Pejman Rasti’, ‘Valentin Gilet’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Notebook
DL@MBL 2021 Exercises#
[‘Jan Funke’, ‘Constantin Pape’, ‘Morgan Schwartz’, ‘Xiaoyan’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
Dask Course#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Python, Bioimage Analysis, Big Data
Content type: Notebook
Deep Learning for image analysis - Exercises#
[‘Martin Weigert’]
Licensed UNKNOWN
Tags: Fiji, Artificial Intelligence, Bioimage Analysis
Content type: Notebook
DeepProfiler Handbook#
[‘Michael Bornholdt’, ‘Juan Caicedo’, ‘Yu Han’, ‘Nikita Moshkov’, ‘Rebecca Senft’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Book
cytomining/DeepProfiler-handbook
https://cytomining.github.io/DeepProfiler-handbook/docs/00-welcome.html
Developing (semi)automatic analysis pipelines and technological solutions for metadata annotation and management in high-content screening (HCS) bioimaging#
[‘Scholz Massei’, ‘Schnike Busch’, ‘Bumberger Bohring’]
Licensed CC-BY-4.0
High-content screening (HCS) bioimaging automates the imaging and analysis of numerous biological samples, generating extensive metadata that is crucial for effective image management and interpretation. Efficiently handling this complex data is essential to implementing FAIR principles and realizing HCS’s full potential for scientific discoveries.
Tags: Bioimage Analysis
Content type: Poster
Diffusion Models for Image Restoration - An Introduction#
[‘Anirban Ray’]
Licensed UNKNOWN
Presentation given at the EMBO-DL4MIA 2024, Advanced Topic Seminar, May-11-2024
Tags: Bioimage Analysis, Diffusion Models, Tu Dresden
Content type: Presentation
https://drive.google.com/file/d/1pPVUUMi5w2Ojw_SaBzSQVaXUuIKtQ7Ma/view
EMBO Practical Course Advanced methods in bioimage analysis#
Tags: Bioimage Analysis
Content type: Event
https://www.embl.org/about/info/course-and-conference-office/events/bia23-01/
EPFLx: Image Processing and Analysis for Life Scientists#
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Online Course
EuBIAS course 2013: Intensity Dynamics at the Periphery of Nucleus#
[‘Kota Miura’]
Published 2013
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Tutorial, Book
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
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
Feature extraction in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/05/03/feature-extraction-in-napari/
Fiji Is Just ImageJ Tutorials#
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/playlist?list=PL5Edc1v41fyCLFZbBCLo41zFO-_cXBfAb
Fit for OMERO: How imaging facilities and IT departments work together to enable RDM for bioimaging#
Starts Oct 16, 2024, 9:00 AM, Ends Oct 17, 2024, 5:00 PM
Tags: Bioimage Analysis, Omero, Research Data Management
Content type: Workshop
Fundamentals in digital image processing#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Notebook
Fundamentals of image analysis in Python with scikit-image, napari, and friends#
[‘Juan Nunez-Iglesias’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Generative artificial intelligence for bio-image analysis#
[‘Robert Haase’]
Licensed CC-BY-4.0
Tags: Python, Bioimage Analysis, Artificial Intelligence
Content type: Slide
Global BioImaging Training Database#
Tags: Bioimage Analysis
Content type: Collection, Event
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
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists#
[‘Gabriel G. Martins’, ‘Fabrice P. Cordelières’, ‘Julien Colombelli’, ‘Rocco D’Antuono’, ‘Ofra Golani’, ‘Romain Guiet’, ‘Robert Haase’, ‘Anna H. Klemm’, ‘Marion Louveaux’, ‘Perrine Paul-Gilloteaux’, ‘Jean-Yves Tinevez’, ‘Kota Miura’]
Published 2021
Licensed CC-BY-4.0
Tags: Bioimage Analysis, Neubias
Content type: Publication
IAFIG-RMS Python for Bioimage Analysis Course#
[‘Aurelien Barbotin’, ‘Chas Nelson’, ‘Dominic Waithe’, ‘Ola (Alexandra) Tarkowska’, ‘Mikolaj Kundegorski’, ‘Stephen Cross’, ‘Todd Fallesen’]
Licensed GPL-3.0
Tags: Bioimage Analysis
Content type: Notebook
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 Analysis Training Resources#
Licensed CC-BY-4.0
Tags: Neubias, Bioimage Analysis
Content type: Book
Image analysis and visualization in Python with scikit-image, napari, and friends#
[‘Juan Nunez-Iglesias’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image analysis in Galaxy#
[‘Beatriz Serrano-Solano’, ‘Björn Grüning’]
Licensed UNKNOWN
Tags: Bioimage Analysis
Content type: Slide
https://docs.google.com/presentation/d/1WG_4307XmKsGfWT3taxMvX2rZiG1k0SM1E7SAENJQkI/edit#slide=id.p
Image processing for beginners#
[‘Guillaume Witz’]
Licensed BSD-3-CLAUSE
Tags: Python, Bioimage Analysis
Content type: Notebook
Image-based Profiling Handbook#
[‘Beth Cimini’, ‘Tim Becker’, ‘Shantanu Singh’, ‘Gregory Way’, ‘Hamdah Abbasi’, ‘Callum Tromans-Coia’]
Licensed CC0-1.0
Tags: Bioimage Analysis
Content type: Book
ImageJ Macro Introduction#
[‘Anna Klemm’]
Licensed UNKNOWN
Tags: Neubias, Imagej Macro, Bioimage Analysis
Content type: Slide, Code
ImageJ2 API-beating#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
Imaris Tutorials#
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Collection, Video
Introduction to Bioimage Analysis#
[‘Pete Bankhead’]
Licensed CC-BY-4.0
Tags: Python, Imagej, Bioimage Analysis
Content type: Book, Notebook
Introduction to Image Analysis with Fiji#
[‘Robert Haase’, ‘Benoit Lombardot’]
Licensed CC-BY-NC-4.0
Tags: Imagej, Fiji, Bioimage Analysis
Introduction to ImageJ macro programming, Scientific Computing Facility, MPI CBG Dresden#
[‘Robert Haase’, ‘Benoit Lombardot’]
Licensed UNKNOWN
Tags: Imagej, Bioimage Analysis
Content type: Slide
Jupyter for interactive cloud computing#
[‘Guillaume Witz’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide
Lecture Applied Bioimage Analysis 2020#
[‘Robert Haase’]
Slides, scripts, data and other exercise materials of the BioImage Analysis lecture at CMCB TU Dresden 2020
Tags: Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_applied_bioimage_analysis
Machine Learning - Deep Learning. Applications to Bioimage Analysis#
[‘Estibaliz Gómez-de-Mariscal’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
Machine Learning Workflow for Imaging Flow Cytometry (IFC)#
Licensed UNKNOWN
Tags: Cellprofiler, Bioimage Analysis
Content type: Tutorial
Machine and Deep Learning on the cloud: Segmentation#
[‘Ignacio Arganda-Carreras’]
Licensed UNKNOWN
Tags: Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slide
Meeting in the Middle: Towards Successful Multidisciplinary Bioimage Analysis Collaboration#
[‘Anjalie Schlaeppi’, ‘Wilson Adams’, ‘Robert Haase’, ‘Jan Huisken’, ‘Ryan B. MacDonald’, ‘Kevin W. Eliceiri’, ‘Elisabeth C. Kugler’]
Licensed CC-BY-4.0
Tags: Bioimage Analysis
Content type: Publication
https://www.frontiersin.org/articles/10.3389/fbinf.2022.889755/full
Melbourne Advanced Microscopy Facility#
Collection of tutorial videos for Fiji users
Tags: Bioimage Analysis
Content type: Collection, Video
Methods in bioimage analysis#
[‘Christian Tischer’]
Licensed CC-BY-4.0
Tags: Bioimage Analysis
Content type: Online Tutorial, Video, Slide
https://www.ebi.ac.uk/training/events/methods-bioimage-analysis/
https://doi.org/10.6019/TOL.BioImageAnalysis22-w.2022.00001.1
https://drive.google.com/file/d/1MhuqfKhZcYu3bchWMqogIybKjamU5Msg/view
MorphoLibJ documentation#
Tags: Bioimage Analysis
Content type: Document
Multi-view fusion#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Lecture slides of a session on Multiview Fusion in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_multiview_registration
NEUBIAS Academy @HOME: Interactive Bioimage Analysis with Python and Jupyter#
Licensed BSD-3-CLAUSE
Tags: Python, Neubias, Bioimage Analysis
Content type: Notebook
NEUBIAS Analyst School 2018#
[‘Assaf Zaritsky’, ‘Csaba Molnar’, ‘Vasja Urbancic’, ‘Richard Butler’, ‘Anna Kreshuk’, ‘Vannary Meas-Yedid’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
NEUBIAS Bioimage Analyst Course 2017#
[‘Curtis Rueden’, ‘Florian Levet’, ‘J.B. Sibarta’, ‘Alexandre Dafour’, ‘Daniel Sage’, ‘Sebastien Tosi’, ‘Michal Kozubek’, ‘Jean-Yves Tinevez’, ‘Kota Miura’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Tutorial
NEUBIAS Bioimage Analyst School 2019#
[‘Kota Miura’, ‘Chong Zhang’, ‘Jean-Yves Tinevez’, ‘Robert Haase’, ‘Julius Hossein’, ‘Pejamn Rasti’, ‘David Rousseau’, ‘Ignacio Arganda-Carreras’, ‘Siân Culley’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
NEUBIAS Bioimage Analyst School 2020#
[‘Marion Louveaux’, ‘Stéphane Verger’, ‘Arianne Bercowsky Rama’, ‘Ignacio Arganda-Carreras’, ‘Estibaliz Gómez-de-Mariscal’, ‘Kota Miura’, ‘et al.’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide, Code, Notebook
NFDI4BIOIMAGE#
[‘Carsten Fortmann.Grote’]
Licensed CC-BY-4.0
Presentation was given at the 2nd MPG-NFDI Workshop on April 18th about e NFDI4BIOIMAGE Consortium, FAIRification of Image (meta)data, Zarr, RFC, Training (TA5), contributing.
Tags: Research Data Management, Bioimage Analysis, Fair-Principles, Zarr, Nfdi4Bioimage
Content type: Slides
NFDI4BIOIMAGE - National Research Data Infrastructure for Microscopy and BioImage Analysis - Online Kick-Off 2023#
[‘Stefanie Weidtkamp-Peters’]
Licensed CC-BY-4.0
NFDI4BIOIMAGE core mission, bioimage data challenge, task areas, FAIR bioimage workflows.
Tags: Research Data Management, Fair-Principles, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
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 - 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
Neubias Academy 2020: Introduction to Nuclei Segmentation with StarDist#
[‘Martin Weigert’, ‘Olivier Burri’, ‘Siân Culley’, ‘Uwe Schmidt’]
Licensed UNKNOWN
Tags: Python, Neubias, Artificial Intelligence, Bioimage Analysis
Content type: Slide, Notebook
OMERO - HCS analysis pipeline using Jupyter Notebooks#
[‘Riccardo Massei’]
Licensed MIT
Material and solutions for the course ‘Bioimage data management and analysis with OMERO’ held in Heidelberg (13th May 2024) - Module 3 (1.45 pm - 3.45 pm): OMERO and Jupyter Notebooks. Main goal of the workflow is to show the potential of JN to perform reproducible image analysis in connection with an OMERO instance. In this specific example, we are performing a simple nuclei segmentation from raw images uploaded in OMERO.
Tags: Teaching, Bioimage Analysis, Notebooks, Python, Omero
Content type: Github Repository
ONBI Image Analysis Course#
[‘Mark Jenkinson’, ‘Jens Rittscher’, ‘Dominic Waithe’]
Licensed GPL-2.0
This repository contains the materials for the University of Oxford DTC ONBI Image Analysis course.
Tags: Python, Bioimage Analysis
Content type: Notebook
Open Image Data Handbook#
[‘Kevin Yamauchi’]
Licensed CC-BY-4.0
Tags: Neubias, Research Data Management, Napari, Python, Bioimage Analysis
Content type: Book, Notebook
PoL Bio-Image Analysis Early Career Bio-image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-Early-Career-Track/intro.html
PoL Bio-Image Analysis GPU Accelerated Image Analysis Training School#
Tags: Bioimage Analysis, Python
Content type: Event, Notebook
https://biapol.github.io/PoL-BioImage-Analysis-TS-GPU-Accelerated-Image-Analysis/intro.html
Prompt Engineering in Bio-image Analysis#
[‘Mara Lampert’]
Tags: Python, Jupyter, Bioimage Analysis, Prompt Engineering, Biabob
Content type: Blog
https://focalplane.biologists.com/2024/07/18/prompt-engineering-in-bio-image-analysis/
Python BioImage Analysis Tutorial#
[‘Jonas Hartmann’]
Licensed MIT
Tags: Python, Bioimage Analysis
Python for Microscopists#
[‘Sreenivas Bhattiprolu’]
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Notebook, Collection
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
Quality assurance of segmentation results#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/04/13/quality-assurance-of-segmentation-results/
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
Rescaling images and pixel (an)isotropy#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/03/02/rescaling-images-and-pixel-anisotropy/
Running Deep-Learning Scripts in the BiA-PoL Omero Server#
[‘Marcelo Zoccoler’]
Licensed CC-BY-4.0
Tags: Python, Artificial Intelligence, Bioimage Analysis
Content type: Blog
https://biapol.github.io/blog/marcelo_zoccoler/omero_scripts/readme.html
Scripts_FilopodyanR - a case study for the NEUBIAS TS7 in Szeged#
[‘Marion Louveaux’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Code
Teaching Bioimage Analysis with Python#
[‘Rafael Camacho’]
Licensed MIT
Tags: Python, Bioimage Analysis
Content type: Tutorial
Teaching ImageJ FIJI#
[‘Rafael Camacho’]
Licensed MIT
Tags: Fiji, Bioimage Analysis
Content type: Tutorial
The Digital Cell: Cell Biology as a Data Science#
[‘Stephen Royle’]
Tags: Bioimage Analysis
Content type: Book
Tracking Theory, TrackMate, and Mastodon#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Lecture slides of a session on Cell Tracking in Fiji
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
Tracking in napari#
[‘Mara Lampert’]
Tags: Python, Napari, Bioimage Analysis
Content type: Blog
https://focalplane.biologists.com/2023/06/01/tracking-in-napari/
Training Deep Learning Models for Vision - Compact Course#
[‘Constantin Pape’, ‘Adrian Wolny’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
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
What is Bioimage Analysis? An Introduction#
[‘Kota Miura’]
Licensed UNKNOWN
Tags: Neubias, Bioimage Analysis
Content type: Slide
https://www.dropbox.com/s/5abw3cvxrhpobg4/20220923_DefragmentationTS.pdf?dl=0
Who you gonna call? - Data Stewards to the rescue#
[‘Vanessa Fuchs’, ‘Aphaia Fiona’, ‘Jens Wendt’, ‘Maximilian Müller’, ‘Mohsen Ahmadi’, ‘Riccardo Massei’, ‘Cornelia Wetzker’]
Licensed CC-BY-4.0
The Data Steward Team of the NFDI4BIOIMAGE consortium presents themselves and the services (including the Helpdesk) that we offer.
Tags: Research Data Management, Bioimage Analysis, Data Stewardship, Nfdi4Bioimage
Content type: Poster
Working with objects in 2D and 3D#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
https://git.mpi-cbg.de/rhaase/lecture_working_with_objects_in_2d_and_3d
Working with pixels#
[‘Robert Haase’]
Licensed BSD-3-CLAUSE
Tags: Neubias, Imagej, Bioimage Analysis
Content type: Slide
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
ZIDAS 2020 Introduction to Deep Learning#
[‘Estibaliz Gómez-de-Mariscal’]
Licensed UNKNOWN
Tags: Artificial Intelligence, Bioimage Analysis
Content type: Slide
[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
[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
[Short Talk] NFDI4BIOIMAGE - A consortium in the National Research Data Infrastructure#
[‘Christian Schmidt’]
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.
Tags: Research Data Management, Bioimage Analysis, Nfdi4Bioimage
Content type: Slides
[Workshop] FAIR data handling for microscopy: Structured metadata annotation in OMERO#
[‘Vanessa Fuchs’, ‘Fiona Aphaia’, ‘Christian Schmidt’, ‘Tom Boissonnet’]
Licensed CC-BY-4.0
How to optimize microscopy data management using structured metadata annotations in OMERO, facilitating organization for processing, analysis, and eventual publication. The focus lies on enhancing data findability and usability through object-oriented organization, integrating OMERO with ImageJ/Fiji for image analysis, and implementing community-accepted metadata standards like REMBI to ensure data reproducibility and reusability.
Tags: Research Data Management, Bioimage Analysis, Omero
Content type: Slides
arivis Vision4D Tutorials#
Licensed ALL RIGHTS RESERVED
Tags: Bioimage Analysis
Content type: Collection, Video
https://www.youtube.com/playlist?list=PLRc9dt9lEZh_SVRC4G5moOvgHuvjPwmv0
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
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