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
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.
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
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.
Introducing OMERO-vitessce: an OMERO.web plugin for multi-modal data#
Michele Bortolomeazzi, Christian Schmidt, Jan-Philipp Mallm
Published 2025-02-07
Licensed CC-BY-4.0
omero-vitessce: an OMERO.web plugin for multi-modal data viewing. OMERO is the most used research data management system (RDM) in the bioimaging domain, and has been adopted as a centralized RDM solution by several academic and research institutions. A main reason for this is the ability to directly view and annotate images from a web-based interface. However, this feature of OMERO is currently underpowered for the visualization of very large or multimodal datasets. These datasets, are becoming a more and more common foundation for biological and biomedical studies, due to the recent developments in imaging, and sequencing technologies which enabled their application to spatial-omics. In order to begin to provide this multimodal-data capability to OMERO, we developed omero-vitessce (NFDI4BIOIMAGE/omero-vitessce), a new OMERO.web plugin for viewing data stored in OMERO with the Vitessce (http://vitessce.io/) multimodal data viewer. omero-vitessce can be installed as an OMERO.web plugin with PiPy (https://pypi.org/project/omero-vitessce/), and allows users to set up interactive visualizations of their images of cells and tissues through interactive plots which are directly linked to the image. This enables the visual exploration of bioimage-analysis results and of multimodal data such as those generated through spatial-omics experiments. The data visualization is highly customizable and can be configured not only through custom configuration files, but also with the graphical interface provided by the plugin, thus making omero-vitessce a highly user-friendly solution for multimodal data viewing. most biological datasets. We plan to extend the interoperability of omero-vitessce with the OME-NGFF and SpatialData file formats to leverage the efficiency of these cloud optimized formats. The three files in this Zenodo Record are all the same poster saved in different format all with high resolution images.
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
Prompt Engineering, Agentic Workflows and Multi-modal Large Language Models#
Robert Haase
Published 2025-01-19
Licensed CC-BY-4.0
In these two slide-decks we explore applications of large language models. In the first slide deck we dive into prompt engineering, function calling and how to build agentic workflows. In the second slide-deck we explore multi-modal large language models focusing on vision language models and image generation models.
[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
datenbiene#
Torsten Stöter
Published 2025-02-02T18:50:20+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Tags: Research Data Management
Content type: Github Repository, Software
omero-arc#
Christoph Moehl, Peter Zentis, Niraj Kandpal
Published 2023-12-18T16:11:04+00:00
Licensed GNU GENERAL PUBLIC LICENSE V3.0
Library to export OMERO projects to ARC repositories
Tags: OMERO, Research Data Management
Content type: Github Repository, Software