Tobias Faehling

Dear Team, thanks for the nice tool you have designed. I have a quite specific question and i don't think I could find this in the documentation... Is it possible...

Mantis viewer export with img_sub_folder = None does not work

1

**Describe the bug** ``` plot_utils.create_mantis_dir( fovs=subset_pixel_fovs, mantis_project_path=os.path.join(base_dir, pixel_output_dir, "mantis"), img_data_path=tiff_dir, mask_output_dir=os.path.join(base_dir, pixel_output_dir, "pixel_masks"), mapping = os.path.join(base_dir, pixel_meta_cluster_remap_name), seg_dir=pixie_seg_dir, mask_suffix="_pixel_mask", seg_suffix_name=seg_suffix, img_sub_folder=None ) ``` The function `plot_utils.create_mantis_dir` fails when `img_sub_folder =...

norm_vals_name or norm_vals_name_post_rownorm

1

**Describe the bug** Variable error in Notebook 2: ``` # run pixel data preprocessing pixie_preprocessing.create_pixel_matrix( fovs, channels, base_dir, tiff_dir, pixie_seg_dir, img_sub_folder=img_sub_folder, seg_suffix=seg_suffix, pixel_output_dir=pixel_output_dir, data_dir=pixel_data_dir, subset_dir=pixel_subset_dir, norm_vals_name_post_rownorm=norm_vals_name, #this variable does not...

GSVA error with ssGSEA

2

After updating to R 4.4.0 and using irGSEA.score with method = "ssGSEA", I get the following error: Error: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object...