Blank segmentation output

[Michaelsqj]

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?

[kikiluvbrains]

Hey there, if you could send me the current data files used if anonymized, I can have a go at looking at debugging this issue.

[1cookspe]

Hi @Michaelsqj, thanks for opening this issue. Thank you @kikiluvbrains for offering to help!

@Michaelsqj, the argument for the -sai flag is expected to be a folder, not a .tif file, so would you be able to run the command again with the path to a folder containing .tif files?

We'll update the method to show a more precise error message in the next update of MIRACL.

[kikiluvbrains]

yeah @Michaelsqj, I believe you need to specify a directory containing .tiff files.