Recently added (10)#

Andor Dragonfly confocal image of BPAE cells stained for actin, IMS file format#

Hoku West-Foyle

Published 2025-01-16

Licensed CC0-1.0

https://zenodo.org/records/14675120

https://doi.org/10.5281/zenodo.14675120


Collaborative Working and Version Control with git[hub]#

Robert Haase

Published 2024-01-10

Licensed CC-BY-4.0

This slide deck introduces the version control tool git, related terminology and the Github Desktop app for managing files in Git[hub] repositories. We furthermore dive into:* Working with repositories* Collaborative with others* Github-Zenodo integration* Github pages* Artificial Intelligence answering Github Issues

Tags: Nfdi4Bioimage, Globias, Research Data Management, Research Software Management

https://zenodo.org/records/14626054

https://doi.org/10.5281/zenodo.14626054


Dataset from InCell 2200 microscope misread as a plate#

Fabien Kuttler, Rémy Dornier

Published 2025-01-30

Licensed CC-BY-4.0

Two dummy datasets are provided in this repository : 

Dataset_Ok : 96 wells, 9 fields of view per well, 4 different channels (DAPI, Cy3, FITC, Brightfield), no Z, no T. The .xcde file of this dataset is correctly read by BioFormats, as the dataset is recognized as a plate, and can be imported on OMERO Dataset_fail: 20 wells, 4 fields of view per well, 5 channels, with one duplicate (DAPI, FITC, Cy3, Cy5 wix 4 , Cy5 wix 5), no Z, no T. The .xcde file of this dataset is not correctly read by BioFormats and no images are imported on OMERO.

BioFormats version: 8.0.1 A discussion thread has been open on this topic.

https://zenodo.org/records/14769820

https://doi.org/10.5281/zenodo.14769820


InCell datasets with mix of 2D and 3D failed to be read#

Fabien Kuttler, Rémy Dornier

Published 2025-01-31

Licensed CC-BY-4.0

The provided dataset contains 2 wells, 4 fields of view, 4 channels, no T but different number of Z according to the channel

Cy3 : 1 Z DAPI : 16 Z FITC : 1 Z Brightfield : 1 Z

The mix 2D/3D is not correctly supported and the .xcde file cannot be read. A discussion thread is already open on that topic. Bio-Formats version : 8.0.1  

https://zenodo.org/records/14777242

https://doi.org/10.5281/zenodo.14777242


Integration of Bioimage and *Omics data resources#

Carsten Fortmann-Grote, Mariana Meireles

Published 2025-02-03

This Poster was presented at the 2025 All Hands Meeting of the NFDI4BIOIMAGE Consortium. It presents the current state of data integration activities at the MPI for Evolutionary Biology. Various data and metadata resources such as the internal image data repository OMERO and the Electronic Lab Notebook System OpenBIS are converted into a RDF Knowledge Graph utilizing a R2RML mapping scheme based on the Ontop-VKG framework. The materialized Knowledge Graph is then served via the QLever SPARQL endpoint and user interface. A graphical query editor (SPARNatural) assists users with no SPARQL knowledge in constructing their queries by selecting triple elements from dropdown menus and other widgets. We also present a benchmark comparison of query response times on 10 selected SPARQL queries run against three different endpoint/triplestore implementations. 

https://zenodo.org/records/14792534

https://doi.org/10.5281/zenodo.14792534


Modular training resources for bioimage analysis#

Christian Tischer, Antonio Politi, Tim-Oliver Buchholz, Elnaz Fazeli, Nicola Gritti, Aliaksandr Halavatyi, Sebastian Gonzalez Tirado, Julian Hennies, Toby Hodges, Arif Khan, Dominik Kutra, Stefania Marcotti, Bugra Oezdemir, Felix Schneider, Martin Schorb, Anniek Stokkermans, Yi Sun, Nima Vakili

Published 2024-12-03

Licensed CC-BY-4.0

Resources for teaching/preparing to teach bioimage analysis

Tags: Neubias, Bioimage Analysis

https://zenodo.org/records/14264885

https://doi.org/10.5281/zenodo.14264885


Optimized cranial window implantation for subcellular and functional imaging in vivo#

Ben Vermaercke

Published 2025-01-13

Licensed CC-BY-4.0

Intravital workshop 15/11/2024

https://zenodo.org/records/14641777

https://doi.org/10.5281/zenodo.14641777


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

Content type: Github Repository, Collection

CellMigrationLab/V4SDB_Winter_School_2025


[CIDAS] Scalable strategies for a next-generation of FAIR bioimaging#

Josh Moore

Published 2025-01-23

Licensed CC-BY-4.0

Talk given at Georg-August-Universität Göttingen Campus Institute Data Science23rd January 2025 https://www.uni-goettingen.de/en/653203.html

Tags: Nfdi4Bioimage

https://zenodo.org/records/14716546

https://doi.org/10.5281/zenodo.14716546


[CMCB] Scalable strategies for a next-generation of FAIR bioimaging#

Josh Moore

Published 2025-01-16

Licensed CC-BY-4.0

CMCB LIFE SCIENCES SEMINARSTechnische Universität Dresden16th January 2025 https://tu-dresden.de/cmcb/crtd/news-termine/termine/cmcb-life-sciences-seminar-josh-moore-german-bioimaging-e-v-society-for-microscopy-and-image-analysis-constance  

Tags: Nfdi4Bioimage

https://zenodo.org/records/14650434

https://doi.org/10.5281/zenodo.14650434