# Collection (86) ## 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 Tags: Include In Dalia Content type: Collection, Publication [https://doi.org/10.1371/journal.pbio.3002167](https://doi.org/10.1371/journal.pbio.3002167) [https://www.bioimagingguide.org/](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) Tags: Exclude From Dalia Content type: Collection, Data [https://www.nature.com/articles/nmeth.2083](https://www.nature.com/articles/nmeth.2083) [https://bbbc.broadinstitute.org/](https://bbbc.broadinstitute.org/) --- ## BIA Seminar Series GloBIAS Licensed UNKNOWN The primary goal of this seminar series is to provide a dynamic platform for bioimage analysts, enabling the community to stay up to date with the latest developments in the field and foster community interactions. The seminars are designed to cater to intermediate and advanced analysts, focusing on practical, high-level content that extends beyond basic instruction. Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection [https://www.globias.org/activities/bia-seminar-series](https://www.globias.org/activities/bia-seminar-series) --- ## Bio Image Analysis Lecture 2020 Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/watch?v=e-2DbkUwKk4&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U](https://www.youtube.com/watch?v=e-2DbkUwKk4&list=PL5ESQNfM5lc7SAMstEu082ivW4BDMvd0U) --- ## Bio-image Analysis ICOB 2023 Tags: Bioimage Analysis, Exclude From Dalia Content type: Workshop, Collection [https://github.com/WeiChenChu/Bioimage_Analysis_ICOB_2023](https://github.com/WeiChenChu/Bioimage_Analysis_ICOB_2023) --- ## Bio-image Analysis Workshop Kioto and Taipei 23/24 Tags: Bioimage Analysis, Include In Dalia Content type: Workshop, Collection [https://github.com/Koushouu/Bioimage-Analysis-Workshop-23-24](https://github.com/Koushouu/Bioimage-Analysis-Workshop-23-24) --- ## Bio-image Analysis Workshop Taipei Tags: Bioimage Analysis, Include In Dalia Content type: Workshop, Collection [https://github.com/Koushouu/Bioimage-Analysis-Workshop-Taipei/](https://github.com/Koushouu/Bioimage-Analysis-Workshop-Taipei/) --- ## Bio.tools database Licensed CC-BY-4.0 Tags: Bioinformatics, Exclude From Dalia Content type: Collection [https://bio.tools/](https://bio.tools/) --- ## BioImage Archive AI Gallery Licensed CC0-1.0 Tags: Bioimage Analysis, Artificial Intelligence, Exclude From Dalia Content type: Collection, Data [https://www.ebi.ac.uk/bioimage-archive/galleries/AI.html](https://www.ebi.ac.uk/bioimage-archive/galleries/AI.html) --- ## BioImage Archive Visual Gallery Licensed CC0-1.0 Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Data [https://www.ebi.ac.uk/bioimage-archive/galleries/visualisation.html](https://www.ebi.ac.uk/bioimage-archive/galleries/visualisation.html) --- ## BioImage Archive Volume EM Gallery Licensed CC0-1.0 Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Data [https://www.ebi.ac.uk/bioimage-archive/galleries/vem.html](https://www.ebi.ac.uk/bioimage-archive/galleries/vem.html) --- ## BioImage Informatics Index Training Materials Licensed ODC-BY-1.0 Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection [https://biii.eu/training-material](https://biii.eu/training-material) --- ## Bioimage Archive Tags: Exclude From Dalia Content type: Collection, Data, Publication [https://www.ebi.ac.uk/bioimage-archive/](https://www.ebi.ac.uk/bioimage-archive/) [https://www.sciencedirect.com/science/article/abs/pii/S0022283622000791](https://www.sciencedirect.com/science/article/abs/pii/S0022283622000791) --- ## Bioimage Model Zoo Licensed UNKNOWN Tags: Bioimage Analysis, Artificial Intelligence, Exclude From Dalia Content type: Collection [https://bioimage.io/](https://bioimage.io/) --- ## Bioimage analysis with Napari Fabrizio Musacchio Licensed CC-BY-ND-SA-4.0 Tags: Python, Napari, Bioimage Analysis, Include In Dalia Content type: Collection [https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/](https://www.fabriziomusacchio.com/teaching/teaching_bioimage_analysis/) --- ## COBA: Center for Open Bioimage Analysis YouTube Channel Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/@cobacenterforopenbioimagea1864](https://www.youtube.com/@cobacenterforopenbioimagea1864) --- ## CZI: Open Science Program Collection Tags: Exclude From Dalia Content type: Collection [https://zenodo.org/communities/eoss](https://zenodo.org/communities/eoss) --- ## Cell Tracking Challenge - 2D Datasets Licensed UNKNOWN Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Data [http://celltrackingchallenge.net/2d-datasets/](http://celltrackingchallenge.net/2d-datasets/) --- ## Cell Tracking Challenge - 3D Datasets Licensed UNKNOWN Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Data [http://celltrackingchallenge.net/3d-datasets/](http://celltrackingchallenge.net/3d-datasets/) --- ## CellTrackColab Guillaume Jacquemet Licensed MIT Tags: Exclude From Dalia Content type: Notebook, Collection [https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2](https://www.biorxiv.org/content/10.1101/2023.10.20.563252v2) [https://github.com/guijacquemet/CellTracksColab](https://github.com/guijacquemet/CellTracksColab) --- ## Center for Microscopy and Image Analysis How-to Guides Tags: Include In Dalia Content type: Collection [https://zmb.dozuki.com/c/Image_Analysis](https://zmb.dozuki.com/c/Image_Analysis) --- ## Chris Halvin YouTube channel Licensed UNKNOWN Tags: Napari, Python, Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/@chrishavlin](https://www.youtube.com/@chrishavlin) [https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1](https://www.youtube.com/playlist?list=PLqbhAmYZU5KxuAcnNBIxyBkivUEiKswq1) --- ## Community-developed checklists for publishing images and image analyses Beth Cimini et al. Licensed BSD-3-CLAUSE 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, Include In Dalia Content type: Notebook, Collection [https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html](https://quarep-limi.github.io/WG12_checklists_for_image_publishing/intro.html) --- ## DL4MicEverywhere Iván Hidalgo, et al. Licensed CC-BY-4.0 Tags: Bioimage Analysis, Exclude From Dalia Content type: Notebook, Collection [https://github.com/HenriquesLab/DL4MicEverywhere](https://github.com/HenriquesLab/DL4MicEverywhere) --- ## DL4Proteins-notebooks Michael Chungyoun, Courtney Thomas, Britnie Carpentier, GabeAu79, puv-sreev, Jeffrey Gray Published 2024-09-04T12:24:24+00:00 Colab Notebooks covering deep learning tools for biomolecular structure prediction and design Tags: Bioinformatics, Exclude From Dalia Content type: Github Repository, Collection [https://github.com/Graylab/DL4Proteins-notebooks](https://github.com/Graylab/DL4Proteins-notebooks) --- ## 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, Exclude From Dalia Content type: Collection, Website, Online Tutorial [https://rdmkit.elixir-europe.org/data_life_cycle](https://rdmkit.elixir-europe.org/data_life_cycle) --- ## 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, Dataplant, Include In Dalia Content type: Collection [https://nfdi4plants.org/nfdi4plants.knowledgebase/index.html](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, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/digitalsreeni](https://www.youtube.com/digitalsreeni) [https://www.youtube.com/watch?v=A4po9z61TME](https://www.youtube.com/watch?v=A4po9z61TME) --- ## 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, Exclude From Dalia Content type: Collection [https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=](https://www.ebi.ac.uk/training/on-demand?facets=type:Course%20materials&query=) --- ## Elastix tutorial Marvin Albert Licensed BSD-3-CLAUSE Tutorial material for teaching the basics of (itk-)elastix for image registration in microscopy images. Tags: Image Registration, Itk, Elastix, Include In Dalia Content type: Notebook, Collection [https://m-albert.github.io/elastix_tutorial/intro.html](https://m-albert.github.io/elastix_tutorial/intro.html) --- ## Euro-BioImaging Communication YouTube Channel Tags: Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/c/eurobioimagingcommunication](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, Exclude From Dalia Content type: Collection, Tutorial [https://zenodo.org/records/11473803](https://zenodo.org/records/11473803) [https://doi.org/10.5281/zenodo.11473803](https://doi.org/10.5281/zenodo.11473803) --- ## FAIR BioImage Data Licensed CC-BY-4.0 Tags: Research Data Management, Fair, Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/watch?v=8zd4KTy-oYI&list=PLW-oxncaXRqU4XqduJzwFHvWLF06PvdVm](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, Include In Dalia Content type: Collection [https://www.go-fair.org/fair-principles/](https://www.go-fair.org/fair-principles/) --- ## Fiji Is Just ImageJ Tutorials Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/playlist?list=PL5Edc1v41fyCLFZbBCLo41zFO-_cXBfAb](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, Include In Dalia Content type: Collection, Tutorial, Video [https://www.ebi.ac.uk/training/online/courses/finding-using-public-data/](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, Include In Dalia Content type: Collection [https://forschungsdaten.info/](https://forschungsdaten.info/) --- ## Forschungsdaten.org Licensed CC-BY-4.0 Research Data Management Wiki in German Tags: Research Data Management, Include In Dalia Content type: Collection [https://www.forschungsdaten.org/](https://www.forschungsdaten.org/) --- ## 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, Exclude From Dalia Content type: Collection, Tutorial [https://training.galaxyproject.org/](https://training.galaxyproject.org/) --- ## GerBI Teaching Resources Link List Licensed UNKNOWN List of training materials by the German BioImaging community provided by facilities, the scientific community, and companies. Tags: Exclude From Dalia Content type: Collection [https://gerbi-gmb.de/resources/teaching-resources/](https://gerbi-gmb.de/resources/teaching-resources/) --- ## Glencoe Software Webinars Chris Allan, Emil Rozbicki Licensed UNKNOWN Example Workflows / usage of the Glencoe Software. Tags: OMERO, Exclude From Dalia Content type: Video, Tutorial, Collection [https://www.glencoesoftware.com/media/webinars/](https://www.glencoesoftware.com/media/webinars/) --- ## Global BioImaging Training Database Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Event [https://globalbioimaging.org/international-training-courses](https://globalbioimaging.org/international-training-courses) --- ## Global BioImaging YouTube channel Tags: Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/GlobalBioImaging](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, Include In Dalia Content type: Collection [https://zenodo.org/doi/10.5281/zenodo.8139353](https://zenodo.org/doi/10.5281/zenodo.8139353) --- ## 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, Exclude From Dalia Content type: Collection [https://gerbi-gmb.de/i3dbio/i3dbio-rdm/i3dbio-bioimage-metadata/](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, Exclude From Dalia Content type: Collection [https://gerbi-gmb.de/i3dbio/i3dbio-teaching/train-mat/bioimagelist/](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, Exclude From Dalia Content type: Collection, Video [https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/](https://www.ibiology.org/online-biology-courses/bioimage-analysis-course/) --- ## Image Data Resources Tags: Exclude From Dalia Content type: Collection, Data, Publication [https://idr.openmicroscopy.org/](https://idr.openmicroscopy.org/) [https://www.nature.com/articles/nmeth.4326](https://www.nature.com/articles/nmeth.4326) --- ## 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, Include In Dalia Content type: Collection [https://datacarpentry.org/image-processing/](https://datacarpentry.org/image-processing/) [https://github.com/datacarpentry/image-processing](https://github.com/datacarpentry/image-processing) --- ## Imaris Tutorials Licensed ALL RIGHTS RESERVED Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://imaris.oxinst.com/tutorials](https://imaris.oxinst.com/tutorials) --- ## 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, Exclude From Dalia Content type: Documentation, Collection [https://guide-kvpairs-scripts.readthedocs.io/en/latest/](https://guide-kvpairs-scripts.readthedocs.io/en/latest/) --- ## Melbourne Advanced Microscopy Facility Collection of tutorial videos for Fiji users Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/@melbourneadvancedmicroscop2617](https://www.youtube.com/@melbourneadvancedmicroscop2617) --- ## 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, Quality Control, Exclude From Dalia Content type: Website, Collection [https://metrics-reloaded.dkfz.de/](https://metrics-reloaded.dkfz.de/) --- ## MicroscopyDB Licensed ALL RIGHTS RESERVED Tags: Exclude From Dalia Content type: Collection [https://microscopydb.io/](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, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/neubias](https://www.youtube.com/neubias) --- ## NFDI4BIOIMAGE - a consortium of the National Research Data Infrastructure NFDI4BIOIMAGE Licensed UNKNOWN Tags: Bioimage Analysis, Research Data Management, Nfdi4Bioimage, Exclude From Dalia Content type: Collection [https://nfdi4bioimage.de/home/](https://nfdi4bioimage.de/home/) --- ## NextFlow core nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow Tags: Python, Exclude From Dalia Content type: Collection [https://nf-co.re/](https://nf-co.re/) --- ## OME Event Database Tags: OMERO, Research Data Management, Exclude From Dalia Content type: Collection, Event [https://www.openmicroscopy.org/events/](https://www.openmicroscopy.org/events/) --- ## OMERO Guide Licensed BSD-2-CLAUSE Tags: OMERO, Include In Dalia Content type: Collection [https://omero-guides.readthedocs.io/en/latest/](https://omero-guides.readthedocs.io/en/latest/) --- ## Omero Deployment examples Licensed BSD-2-CLAUSE Tags: OMERO, Include In Dalia Content type: Collection [https://github.com/ome/omero-deployment-examples](https://github.com/ome/omero-deployment-examples) --- ## 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, Exclude From Dalia Content type: Video, Collection [https://www.youtube.com/@OpenMicroscopyEnvironment](https://www.youtube.com/@OpenMicroscopyEnvironment) --- ## 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, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/OpenMicroscopyEnvironment](https://www.youtube.com/OpenMicroscopyEnvironment) --- ## Python for Microscopists Sreenivas Bhattiprolu Licensed MIT Tags: Python, Bioimage Analysis, Include In Dalia Content type: Notebook, Collection [https://github.com/bnsreenu/python_for_microscopists](https://github.com/bnsreenu/python_for_microscopists) --- ## 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, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/qupath/i2k-qupath-for-python-programmers](https://github.com/qupath/i2k-qupath-for-python-programmers) --- ## RDM4Mic Presentations Licensed CC-BY-4.0 Tags: Research Data Management, Exclude From Dalia Content type: Collection [https://github.com/German-BioImaging/RDM4mic/tree/master/presentations](https://github.com/German-BioImaging/RDM4mic/tree/master/presentations) --- ## RDM4mic Licensed UNKNOWN Tags: Research Data Management, OMERO, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/@RDM4mic](https://www.youtube.com/@RDM4mic) --- ## RDMBites BioImage metadata Tags: Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/watch?v=aRHNHk07t3Q&list=PLyCNTVs-UBvuJF7WausQ5q7v7pI1vEpI1](https://www.youtube.com/watch?v=aRHNHk07t3Q&list=PLyCNTVs-UBvuJF7WausQ5q7v7pI1vEpI1) --- ## RDMKit Training Resources Licensed CC-BY-4.0 Tags: Research Data Management, Include In Dalia Content type: Collection [https://rdmkit.elixir-europe.org/all_training_resources](https://rdmkit.elixir-europe.org/all_training_resources) --- ## 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, Research Data Management, Include In Dalia Content type: Collection [https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/](https://www.ebi.ac.uk/bioimage-archive/rembi-help-overview/) --- ## 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, Exclude From Dalia Content type: Collection [https://www.nature.com/collections/djiciihhjh](https://www.nature.com/collections/djiciihhjh) --- ## 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: Include In Dalia Content type: Collection, Online Course, Video, Tutorial [https://software-skills.neuroinformatics.dev/index.html](https://software-skills.neuroinformatics.dev/index.html) --- ## TESS Event database Tags: Bioinformatics, Exclude From Dalia Content type: Collection, Event [https://tess.elixir-europe.org/events](https://tess.elixir-europe.org/events) --- ## TESS training materials Licensed UNKNOWN Tags: Bioinformatics, Exclude From Dalia Content type: Collection [https://tess.elixir-europe.org/materials](https://tess.elixir-europe.org/materials) --- ## Tess Search for Data Life Cycle Licensed UNKNOWN Tags: Data Life Cycle, Research Data Management, Exclude From Dalia Content type: Collection [https://tess.elixir-europe.org/search?q=data+life+cycle#materials](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, Exclude From Dalia Content type: Collection, Event, Forum Post, Workshop [https://forum.image.sc/t/upcoming-image-analysis-events/60018/67](https://forum.image.sc/t/upcoming-image-analysis-events/60018/67) --- ## V4SDB_Winter_School_2025 Joanna Pylvänäinen Published 2025-01-13T08:29:22+00:00 Training materials for V4SDB Student Winter School, 28th-31st January 2025 at ELTE Eötvös Loránd University in Budapest, Hungary Tags: Cell Tracking, Bioimage Analysis, Exclude From Dalia Content type: Github Repository, Collection [https://github.com/CellMigrationLab/V4SDB_Winter_School_2025](https://github.com/CellMigrationLab/V4SDB_Winter_School_2025) --- ## WebAtlas pipeline for integrated single cell and spatial transcriptomic data Tong Li, David Horsfall, Daniela Basurto-Lozada Published 2023-04-28 Licensed None Single cell and spatial transcriptomics illuminate complementary features of tissues. However, the online dissemination and exploration of multi-modal datasets is challenging. We introduce the WebAtlas pipeline for user-friendly sharing and interactive navigation of integrated datasets. WebAtlas unifies commonly used atlassing technologies into the cloud-optimised Zarr format and builds on Vitessce to enable remote data navigation. We showcase WebAtlas on the developing human lower limb to cross-query cell types and genes across single cell, sequencing- and imaging-based spatial transcriptomic data. Tags: Spatial Transcriptomics, Single Cell, Bioimage Analysis, Exclude From Dalia Content type: Collection, Atlas [https://developmental.cellatlas.io/webatlas](https://developmental.cellatlas.io/webatlas) [https://www.biorxiv.org/content/10.1101/2023.05.19.541329v1](https://www.biorxiv.org/content/10.1101/2023.05.19.541329v1) --- ## 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, Include In Dalia Content type: Collection [http://opendatahandbook.org/guide/en/what-is-open-data/](http://opendatahandbook.org/guide/en/what-is-open-data/) --- ## 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, Exclude From Dalia Content type: Collection [https://workflowhub.eu/](https://workflowhub.eu/) --- ## Workshop-June2024-Madrid Licensed MIT Tags: Bioimage Analysis, Exclude From Dalia Content type: Workshop, Collection [https://github.com/bioimage-io/Workshop-June2024-Madrid](https://github.com/bioimage-io/Workshop-June2024-Madrid) --- ## ZEN & Python workshop Licensed GPL-3.0 Tags: Python, Napari, Bioimage Analysis, Include In Dalia Content type: Collection, Notebook [https://github.com/zeissmicroscopy/ZEN_Python_OAD_workshop](https://github.com/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 Tags: Bioimage Analysis, Exclude From Dalia Content type: Notebook, Collection [https://github.com/HenriquesLab/ZeroCostDL4Mic](https://github.com/HenriquesLab/ZeroCostDL4Mic) [https://www.nature.com/articles/s41467-021-22518-0](https://www.nature.com/articles/s41467-021-22518-0) [https://doi.org/10.1038/s41467-021-22518-0](https://doi.org/10.1038/s41467-021-22518-0) --- ## arivis Vision4D Tutorials Licensed ALL RIGHTS RESERVED Tags: Bioimage Analysis, Exclude From Dalia Content type: Collection, Video [https://www.youtube.com/playlist?list=PLRc9dt9lEZh_SVRC4G5moOvgHuvjPwmv0](https://www.youtube.com/playlist?list=PLRc9dt9lEZh_SVRC4G5moOvgHuvjPwmv0) --- ## imagequantification101 Virginie, Guillaume Witz, Joel Lüthi Published 2022-08-17T14:55:16+00:00 Licensed BSD-3-CLAUSE Tags: Bioimage Analysis, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/uhlmanngroup/imagequantification101](https://github.com/uhlmanngroup/imagequantification101) --- ## microlist Licensed ALL RIGHTS RESERVED A searchable database of resources for light and electron microscopists Tags: Exclude From Dalia Content type: Collection [https://www.microlist.org/](https://www.microlist.org/) --- ## shapeanalysis101 Virginie, Johannes Hugger Published 2021-05-17T13:32:40+00:00 Licensed BSD-3-CLAUSE A tutorial of classical shape analysis methods Tags: Bioimage Analysis, Include In Dalia Content type: Github Repository, Notebook, Collection [https://github.com/uhlmanngroup/shapeanalysis101](https://github.com/uhlmanngroup/shapeanalysis101) ---