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haniffalab / webatlas-pipeline

A data pipeline built in Nextflow to process spatial and single-cell experiment data for visualisation in WebAtlas
MIT License
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Using PNG raw images results in distorted color scheme #106

Open d-goryslavets opened 1 year ago

d-goryslavets commented 1 year ago

After processing raw image in PNG format and visualizing the output data in WebAtlas app, the colors of the displayed image differ from the original.

Visualization of a TIF tissue image: tif

Visualization of its downscaled PNG version: png

prete commented 1 year ago

Hi @d-goryslavets can you share links to both visualizations? Based on the screenshots, the channels are not set to the same colors and that may be the issue?

d-goryslavets commented 1 year ago

Sure. I currently run the application locally on farm, so please access it via

http://node-11-10-2.internal.sanger.ac.uk:8000/?config=http://node-11-10-1.internal.sanger.ac.uk:3000/thymus_project-thymus_visium-config.json (PNG)

http://node-11-10-2.internal.sanger.ac.uk:8000/?config=http://node-11-10-2.internal.sanger.ac.uk:3000/thymus_project-thymus_visium-config.json (TIF)

BioinfoTongLI commented 10 months ago

this seems to be just a matter of different dynamic range that had been selected for different channels OR RGB vs. blue-green-magenta-yellow color schem.