Collection (57)#

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

https://doi.org/10.1371/journal.pbio.3002167

https://www.bioimagingguide.org/

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

https://www.nature.com/articles/nmeth.2083

https://bbbc.broadinstitute.org/

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

WeiChenChu/Bioimage_Analysis_ICOB_2023

Bio-image Analysis Workshop Kioto and Taipei 23/24#

Tags: Bioimage Analysis

Content type: Workshop, Collection

Koushouu/Bioimage-Analysis-Workshop-23-24

Bio-image Analysis Workshop Taipei#

Tags: Bioimage Analysis

Content type: Workshop, Collection

Koushouu/Bioimage-Analysis-Workshop-Taipei

Bio.tools database#

Licensed CC-BY-4.0

Tags: Bioinformatics

Content type: Collection

https://bio.tools/

BioImage Informatics Index Training Materials#

Licensed ODC-BY-1.0

Tags: Bioimage Analysis

Content type: Collection

https://biii.eu/training-material

Bioimage Archive#

Content type: Collection, Data, Publiction

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

https://bioimage.io/

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

https://www.youtube.com/@cobacenterforopenbioimagea1864

CZI: Open Science Program Collection#

Content type: Collection

https://zenodo.org/communities/eoss

Cell Tracking Challenge - 2D Datasets#

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Collection, Data

http://celltrackingchallenge.net/2d-datasets/

Cell Tracking Challenge - 3D Datasets#

Licensed UNKNOWN

Tags: Bioimage Analysis

Content type: Collection, Data

http://celltrackingchallenge.net/3d-datasets/

CellTrackColab#

[‘Guillaume Jacquemet’]

Licensed MIT

Content type: Notebook, Collection

https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2

guijacquemet/CellTracksColab

Center for Microscopy and Image Analysis How-to Guides#

Content type: Collection

https://zmb.dozuki.com/c/Image_Analysis

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

DL4MicEverywhere#

[‘Iván Hidalgo’, ‘et al.’]

Licensed CC-BY-4.0

Content type: Notebook, Collection

HenriquesLab/DL4MicEverywhere

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

https://www.youtube.com/digitalsreeni

https://www.youtube.com/watch?v=A4po9z61TME

Euro-BioImaging Communication YouTube Channel#

Content type: Collection, Video

https://www.youtube.com/c/eurobioimagingcommunication

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

https://zenodo.org/records/11473803

https://doi.org/10.5281/zenodo.11473803

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

Fiji Is Just ImageJ Tutorials#

Tags: Bioimage Analysis

Content type: Collection, Video

https://www.youtube.com/playlist?list=PL5Edc1v41fyCLFZbBCLo41zFO-_cXBfAb

Forschungsdaten.info#

Licensed PUBLIC DOMAIN

Research Data Management Information Portal in German

Tags: Research Data Management

Content type: Collection

https://forschungsdaten.info/

Forschungsdaten.org#

Licensed CC-BY-4.0

Research Data Management Wiki in German

Tags: Research Data Management

Content type: Collection

https://www.forschungsdaten.org/

Global BioImaging Training Database#

Tags: Bioimage Analysis

Content type: Collection, Event

https://globalbioimaging.org/international-training-courses

Global BioImaging YouTube channel#

Content type: Collection, Video

https://www.youtube.com/GlobalBioImaging

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

https://zenodo.org/doi/10.5281/zenodo.8139353

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

https://idr.openmicroscopy.org/

https://www.nature.com/articles/nmeth.4326

Imaris Tutorials#

Licensed ALL RIGHTS RESERVED

Tags: Bioimage Analysis

Content type: Collection, Video

https://imaris.oxinst.com/tutorials

Melbourne Advanced Microscopy Facility#

Collection of tutorial videos for Fiji users

Tags: Bioimage Analysis

Content type: Collection, Video

https://www.youtube.com/@melbourneadvancedmicroscop2617

MicroscopyDB#

Licensed ALL RIGHTS RESERVED

Content type: Collection

https://microscopydb.io/

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

https://www.youtube.com/neubias

NextFlow core#

nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow

Tags: Python

Content type: Collection

https://nf-co.re/

OME Event Database#

Tags: Omero, Research Data Management

Content type: Collection, Event

https://www.openmicroscopy.org/events/

OMERO Guide#

Licensed BSD-2-CLAUSE

Tags: Omero

Content type: Collection

https://omero-guides.readthedocs.io/en/latest/

Omero Deployment examples#

Licensed BSD-2-CLAUSE

Tags: Omero

Content type: Collection

ome/omero-deployment-examples

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

https://www.youtube.com/OpenMicroscopyEnvironment

Python for Microscopists#

[‘Sreenivas Bhattiprolu’]

Licensed MIT

Tags: Python, Bioimage Analysis

Content type: Notebook, Collection

bnsreenu/python_for_microscopists

RDM4Mic Presentations#

Licensed CC-BY-4.0

Tags: Research Data Management

Content type: Collection

German-BioImaging/RDM4mic

RDM4mic#

Licensed UNKNOWN

Tags: Research Data Management, Omero

Content type: Collection, Video

https://www.youtube.com/@RDM4mic

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

https://rdmkit.elixir-europe.org/all_training_resources

TESS Event database#

Tags: Bioinformatics

Content type: Collection, Event

https://tess.elixir-europe.org/events

TESS training materials#

Licensed UNKNOWN

Tags: Bioinformatics

Content type: Collection

https://tess.elixir-europe.org/materials

Workshop-June2024-Madrid#

Licensed MIT

Tags: Bioimage Analysis

Content type: Workshop, Collection

bioimage-io/Workshop-June2024-Madrid

ZEN & Python workshop#

Licensed GPL-3.0

Tags: Python, Napari, Bioimage Analysis

Content type: Collection, Notebook

zeissmicroscopy/ZEN_Python_OAD_workshop

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

HenriquesLab/ZeroCostDL4Mic

https://www.nature.com/articles/s41467-021-22518-0

https://doi.org/10.1038/s41467-021-22518-0

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

https://www.microlist.org/