help wanted
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説明
I tried to segment my own lsm data. for starter I tried a small block but the generated segmentation are all blank.
here's the command I run in the apptainer.
miracl seg ace -sai /data/200316-1-1_N12_N58204NLSAM_NeuN-ls_M4D/chunk_0_start_1767_4325_941_end_2192_3858_1159.tif -sao /data/outputs/ -sam unet -sar 1.8 1.8 4.0
In the input folder, I have slice_z001.tif to slice_z218.tif, 218 slices in total. each slice has shape (425, 467).
I got seg_final folder, and generated_patches with.
out_patch_0_0.tiff
patch_0_0.tiff
percentage_brain_patch.json
the percentage_brain_patch.json is
{
"patch_0_0.tiff": 7.688754051923752
}
The out_patch_0_0.tiff has size 512,512,512 and completely blank.
May I ask is there any requirements for the input data? what might cause the issue of having blank segmention output?