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chaichontat / samui

A performant scientific image visualization system.
https://samuibrowser.com/
GNU General Public License v3.0
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instructions on how to generate data for Vizgen MERFISH data #80

Closed IrinaVKuznetsova closed 1 year ago

IrinaVKuznetsova commented 1 year ago

Dear developers,

Could you please provide more instructions on how to generate and explore data for Vizgen MERFISH data on Sumai web browser.

I managed to convert TIFF files to COG. I can upload the sample folder to the browser, but I cant explore genes on the image Used process_merfish.py script to generate a folder with sample.json; X.tif, cell.json; cells.bin and cellCoordinates.csv , but still unable to explore genes on the image none of selected genes are highlighted on the image (please see below). Thank you

Test17March (1)

chaichontat commented 1 year ago

Hi, could you send me the sample files via email? I'll need the cell by gene matrix, cell coordinates, and the coordinate transformation matrix.

From the image, the gene data was loaded correctly. My guess is that the transformation that aligns the cell and image coordinates or the image scale are off.

chaichontat commented 1 year ago

I fixed the scaling in commit 2ee97518060edcb226d7dc33d152984cc5720dc5 and separated the image and spot parts so that at least users can get something if the scaling does not work.

image