Identifies cell outlines, counts number of spots in each cell, and saves counts and ROIs to OMERO.
- Details for connecting to an OMERO server.
- OMERO dataset ID containting image stacks with at least 2 channels.
- Install Fiji
- Install OMERO for ImageJ Plugin
- Install simple-omero-clients
- Install omero_macro-extensions
- Install MorphLibJ
Instructions for installing the OMERO Plugins are available here: https://omero-guides.readthedocs.io/projects/fiji/en/latest/installation.html
Instructions for installing the MorphoLibJ plugins are available here: https://imagej.net/plugins/morpholibj
Saves ROIs for nuclei and spots to OMERO images and saves NumberSpotsInCells.csv to each image. A single .csv file is saved to the dataset. The results file contains three columns: 1) the image ID; 2)the cell ID which relates to the ROI and 3) the number of spots in that cell.
Legland, D., Arganda-Carreras, I., & Andrey, P. (2016). MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics, 32(22), 3532–3534. doi:10.1093/bioinformatics/btw413
Pouchin P, Zoghlami R, Valarcher R et al. Easing batch image processing from OMERO: a new toolbox for ImageJ [version 2; peer review: 2 approved]. F1000Research 2022, 11:392 (https://doi.org/10.12688/f1000research.110385.2)