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How to build a semla object without h5 file？ #8

Closed Cambyses-Chen closed 1 year ago

Cambyses-Chen commented 1 year ago

Dear authors of semla. Thank you for developing such an excellent spatial transcriptome analysis software as semla. I only have filtered_count_matrices folder with 3 files, no h5 files. How should I construct a semla object？ I have other files "aligned_fiducials.jpg", "detected_tissue_image.jpg", "scalefactors_json.json", "tissue_hires_image.png", "tissue_positions_list.csv". Thank you for the help.

ludvigla commented 1 year ago

Hi!

I just pushed a minor fix to make it possible to load the filtered_count_matrices folder instead of the h5 files.

When you construct the infoTable for ReadVisiumData you can just place the filtered_count_matrices folder paths in the samples column and it should work now.

Just make sure to install the latest dev version of semla.

Cheers, Ludvig

Cambyses-Chen commented 1 year ago

Hi!

I just pushed a minor fix to make it possible to load the filtered_count_matrices folder instead of the h5 files.

When you construct the infoTable for ReadVisiumData you can just place the filtered_count_matrices folder paths in the samples column and it should work now.

Just make sure to install the latest dev version of semla.

Cheers, Ludvig Thank you so much！I will try the method you provide.

Cambyses-Chen commented 1 year ago

This problem has been solved, thanks to Ludvig.