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ome / omero-parade

OMERO.web plugin for displaying Dataset thumbnails or Plates in webclient center panel
GNU Affero General Public License v3.0
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Parade for histo cytometry application #96

Open matfallet opened 2 years ago

matfallet commented 2 years ago

I was wondering if parade was able to process quite easily histo cytometry application (with dataset for different condition/activation on Omero) if the segmentation results is given as mask (to extract results) ? Scatterplot are interactive in parade with the image isn't-it so it seems quite powerful for that ?

will-moore commented 2 years ago

You need to have images in OMERO with numerical values associated with each Image. For example, these values could be in a csv file linked to the parent Project, with an Image ID on each row. These numbers could be generated from segmentation results, but this will probably have to be done by some external application, not by OMERO itself.

E.g. a demo of parade using measurements from FiJi: https://www.youtube.com/watch?v=Bmi31J04A_E Also see some docs for this demo: https://omero-guides.readthedocs.io/en/latest/parade/docs/omero_parade.html

matfallet commented 2 years ago

Thanks for your answer. Just a little precision : if I generate theses datas (csv, roi,), parade could be used easily for set of images or is it designed for box (96 wells,...) ? Can you do multiple scatterplot like for cytometry or maybe this a point you will develop later ?

will-moore commented 2 years ago

It can be used for any set of Images. E.g. see in the demo movie on the idr0021 data. You can't do multiple scatter plots in omero-parade.

However, I have done some work on a side-project to investigate potential new features: https://github.com/will-moore/parade-crossfilter. This isn't very well tested yet (and isn't supported by the OME team) but it does support multiple scatter plots. See demo https://youtu.be/XvbHczzePSo?t=69