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Question: Source for "Whole Slide Image" .btf file? #21

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jade-minzlaff opened this issue Jan 3, 2025 · 0 comments
Open

Question: Source for "Whole Slide Image" .btf file? #21

jade-minzlaff opened this issue Jan 3, 2025 · 0 comments

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@jade-minzlaff
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jade-minzlaff commented Jan 3, 2025

@Mena-SA-Kamel Hello, I am attempting to run the ENACT pipeline on my data, but the tutorial uses a .btf file listed as "Whole Slide Image". I have done the standard Visium HD workflow and Spaceranger pre-processing. In the Spaceranger output for my data, I don't see any image files of this file type. I have aligned_fiducials.jpg, aligned_tissue_image.jpg, cytassist_image.tiff, detected_tissue_image.jpg, tissue_hires_image.png, and tissue_lowres_image.png. I attempted to run the ENACT pipeline using the cytassist_image.tiff file, but I ran into an assertion error when I tried to run the code, as the size of the image file was wrong. Will any of the image files I have work for ENACT, and if not, how do I generate a "whole tissue image" .btf file for my data?

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