diff --git a/workflow/config/visium_hd/cellpose.yaml b/workflow/config/visium_hd/cellpose.yaml deleted file mode 100644 index caadbf1..0000000 --- a/workflow/config/visium_hd/cellpose.yaml +++ /dev/null @@ -1,21 +0,0 @@ -# For parameters details, see this commented example: https://github.com/gustaveroussy/sopa/blob/master/workflow/config/example_commented.yaml -read: - technology: visium_hd - -patchify: - patch_width_pixel: 2000 - patch_overlap_pixel: 50 - -segmentation: - cellpose: - diameter: 15 - channels: ["r"] # first channel of the H&E image - min_area: 50 - -aggregate: - aggregate_channels: false - aggregate_genes: true - min_transcripts: 10 # [optional] cells whose transcript count is below that this threshold are filtered - -explorer: - ram_threshold_gb: 4