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@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?
The text was updated successfully, but these errors were encountered:
@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?
The text was updated successfully, but these errors were encountered: