Test datasets for omero-vitessce

Dataset designed for testing the omero-vitessce (https://github.com/NFDI4BIOIMAGE/omero-vitessce) plugin for OMERO (https://www.openmicroscopy.org/omero/). The omero-vitessce repository contains a cropped version of this dataset for automated testing (https://github.com/NFDI4BIOIMAGE/omero-vitessce/tree/main/test/data/MB266).

Files

• MAX_MBEN_ff_Xenium_0018446_MB-266_DAPI_2024-01-23_12.47.34_Fused_405nm_corr_cropped.png = PNG image with the DAPI channel.
• MAX_MBEN_ff_Xenium_0018446_MB-266_DAPI_2024-01-23_12.47.34_Fused_405nm_corr_cropped_cp_masks.png= Cell segmentation mask pixel values correspond to cell identities, 0 = background).
• cells.csv = 
• embeddings.csv = UMAP embeddings for drawing an interactive scatterplot.
• feature_matrix.csv = Transcript counts in each cell.
• transcripts.csv = Gene name and coordinates (pixel) of each transcript.
• VitessceConfig.json = Example configuration file generated by the omero-vitessce plugin for the Vitessce, an equivalent file can be generated by using the form provided by the plugin in OMERO.web.

See the repository README file for more details on the formats of these files: https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#config-files

Usage

1. Add the omero-web-zarr and omero-vitessce plugins to your OMERO.web installation.
2. Import the images into OMERO in the same dataset.
3. Attach all the .csv data files.
4. Use the form in the "Vitessce" tab of the right-panel to generate a configuration file and open the Vitessce viewer.

See the repository README file for more details on usage (https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#usage) and installation (https://github.com/NFDI4BIOIMAGE/omero-vitessce?tab=readme-ov-file#installation)

Data Sources

Adapted from the full original data at: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1093 (10.6019/S-BIAD1093).

The original data were produced and analysed in the course of this study:

https://www.biorxiv.org/content/10.1101/2024.04.03.586404v1