Recently added (10)#
“Management of Microscopy Image Data: An overview of OMERO, BioImage Archive and Image Data Resource” 2025 @ Uni Leipzig#
Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
Published 2025-08-15
Licensed CC-BY-4.0
Presentation matherial from the course “Management of Microscopy Image Data: An Overview of OMERO, BioImage Archive and Image Data Resource” helded in Uni Leipzig on the 04/07/2025. This course is part of the RDM lecture series organized by Dr. Dr. habil. Dagmar Quandt. Link to the event: https://fortbildung.uni-leipzig.de/fortbildung.html?id=2436 M. Massei is funded by the Deutsche Forschungsgemeinschaft (DFG) – project number [NFDI46/1] - 501864659
Cloud-Native Formats Enable Federated Repositories at Peta-Scale#
Josh Moore
Published 2025-09-27
Licensed CC-BY-4.0
Poster presentation for the abstract “Enabling Peta-Scale Federated Repositories through Cloud-Native Formats: Lessons from a fast-paced challenge in the bioimaging community” submitted to 2nd Conference on Research Data Infrastructure (CoRDI) 2025
DCIMG dense beads taken in chunks over time#
Zach Marin
Published 2025-08-14
Licensed CC-BY-4.0
Two 2000-frame chunks acquired at different times (~40 minutes apart) on a 4Pi widefield, showing some slow sample drift.
Euro-BioImaging Annual Report 2024#
Euro-BioImaging ERIC
Published 2025-06-30
Licensed CC-BY-4.0
Euro-BioImaging ERIC is the European landmark research infrastructure for biological and biomedical imaging as recognized by the European Strategy Forum on Research Infrastructures (ESFRI). Euro-BioImaging is the gateway to world-class imaging facilities across Europe. This document is the Euro-BioImaging Annual Report for the year 2024.
ImageJ Bioformats 8.3.0 Importer Incorrectly Reading ND2 Metadata#
Snyder, Erika, Erika Thomas, Erika T.
Published 2025-08-21
Licensed CC-BY-4.0
Hi all,I was referred to this community from the Image.sc Forum original post: https://forum.image.sc/t/imagej-bioformats-importer-incorrectly-reading-metadata/115943 I have an ND2 file, 3 color channels, 2 positions in the well, and 81 timepoints. However, when I open this as I normally would in ImageJ as a hyperstack, the stack interpretation is totally incorrect. It is including my Z-positions as frames in the timelapse. Even when I open the series for the positions independently, images from the other series will appear within it. I am running Bioformats 8.3.0. I have tried swapping dimensions. That did not work. I have tried creating substacks to parse out one series from the other, this also did not work. The only thing I can think of that is different from before is that I was previously aquiring z-stacks with our MCL nanodrive Piezo, and we had to have that serviced so in the meantime I used the Ti2 eclipse camera drive for z-stack aquisiton. I have opened the metadata to compare aquisitions between the two, and the stack order appears exactly the same, although Bioformats has no problem reading the metadata for aquisitions with the Piezo. I have also opened this file in NIS elements viewer, and all the information for the stacks appears correctly, so I dont think aquisitions is the issue. I have also tried opening this file on multiple computers with multiple versions of imageJ, and the issue persists. Any advice would be greatly appreciated I am panicking a bit because this is a few months worth of data I am suddenly not able to analyze. Please let me know if there’s anything else needed to help figure this out.
Images acquired with Zeiss Sigma 300 - Images with low magnification are corrently not handeled correctly#
Johannes Preußner
Published 2025-08-07
Licensed CC-BY-4.0
When using bioformats the images are not scaled correctly. The problem arises with low magnifications where the lengths in the metadata are given in µm (not in nm). Attached are two pictures. Only with the picture with the ending “Correct_scale_bar” the import is working correctly. One issue might be that the metadata information of the images are stored in iso-8859-1
Laser perturbation imaging data for: Patterned invagination prevents mechanical instability during gastrulation#
Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
Published 2025-07-14
Licensed CC-BY-4.0
This repository contains the imaging data for the laser perturbation experiments of the manuscript: Vellutini BC, Cuenca MB, Krishna A, Szałapak A, Modes CD, Tomančák P. Patterned embryonic invagination evolved in response to mechanical instability. bioRxiv (2023) doi:10.1101/2023.03.30.534554 Please refer to the main repository for more information: https://doi.org/10.5281/zenodo.7781947
Lightsheet and in situ imaging data for: Patterned invagination prevents mechanical instability during gastrulation#
Vellutini, Bruno C., Cuenca, Marina B., Abhijeet Krishna, Alicja Szałapak, Modes, Carl D., Pavel Tomančák
Published 2025-07-14
Licensed CC-BY-4.0
This repository contains the lightsheet and in situ hybridization imaging data for the manuscript: Vellutini BC, Cuenca MB, Krishna A, Szałapak A, Modes CD, Tomančák P. Patterned embryonic invagination evolved in response to mechanical instability. bioRxiv (2023) doi:10.1101/2023.03.30.534554 Please refer to the main repository for more information: https://doi.org/10.5281/zenodo.7781947
Model and simulations for: Patterned invagination prevents mechanical instability during gastrulation#
Abhijeet Krishna, Alicja Szałapak, Vellutini, Bruno C., Cuenca, Marina B., Pavel Tomančák, Modes, Carl D.
Published 2025-07-14
Licensed CC-BY-4.0
This repository contains the code and simulations for the manuscript: Vellutini BC, Cuenca MB, Krishna A, Szałapak A, Modes CD, Tomančák P. Patterned embryonic invagination evolved in response to mechanical instability. bioRxiv (2023) doi:10.1101/2023.03.30.534554 Please refer to the main repository for more information: https://doi.org/10.5281/zenodo.7781947
Repository for: Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning#
Vellutini, Bruno C., Martín-Durán, José M., Aina Børve, Andreas Hejnol
Published 2024-08-16
Licensed CC-BY-4.0
This repository contains the data and analyses for the manuscript: Vellutini, B. C., Martín-Durán, J. M., Børve, A. & Hejnol, A. Combinatorial Wnt signaling landscape during brachiopod anteroposterior patterning. BMC Biol. 22, 1–23 (2024). https://doi.org/10.1186/s12915-024-01988-w The source is maintained at bruvellu/terebratalia-wnts.
https://zenodo.org/records/13338425
https://doi.org/10.5281/zenodo.13338425