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Nanostring-Biostats / CosMx-Analysis-Scratch-Space

This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
https://nanostring-biostats.github.io/CosMx-Analysis-Scratch-Space/
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Custom Stitching of Selected FOVs in the Napari-CosMx Plugin? #106

Closed keiven-kun closed 1 month ago

keiven-kun commented 1 month ago

Hi,

Thank you for introducing the "napari-cosmx plugin" in the Nanostring Blog.

Following the steps outlined in the blog, I successfully created a napari-ready slide file from AtoMx raw data using the "stitching widget" method. However, the resulting napari file contains all the FOVs in one slide. In my CosMx experiment, I have several unrelated samples on a single slide, and I would like to view them separately in napari.

Is there a way to stitch only the selected FOVs (e.g., FOVs 10–30) together and create a napari-ready file from the raw data?

Thank you very much for your assistance!

eveilyeverafter commented 1 month ago

Look for the latest.fovs.csv file in the RunSummary folder and remove unwanted fovs. You may want to make a copy of the original csv.

keiven-kun commented 1 month ago

Thank you for your prompt response. It worked perfectly! I really appreciate it.