nilseling
commented
1 year ago Hi @giuliospinozzi
In the deepcell column you would need to put a 1 for channels which are nuclear and a 2 for channels which are cytoplasmic. Please close this issue if it worked for you.
I'am trying to use Steinbock for segmentation (DeepCell/Mesmer) but this error occurs:
2023-07-04 08:16:02,041 ERROR steinbock.segmentation.deepcell - Error segmenting objects in img/22E594A1_2_014.tiff: Invalid number of aggregated channels: expected 2, got 36 Traceback (most recent call last): File "/app/steinbock/steinbock/segmentation/deepcell.py", line 130, in try_segment_objects raise SteinbockDeepcellSegmentationException( steinbock.segmentation.deepcell.SteinbockDeepcellSegmentationException: Invalid number of aggregated channels: expected 2, got 36
Before that command (steinbock segment deepcell --minmax) I used: steinbock preprocess imc panel steinbock preprocess imc images --hpf 50
Can you help me to solve this issue? I started from MCD file. The panel and the images were created well...
Thanks a lot. Giulio
Here the panel: channel,name,keep,ilastik,deepcell,cellpose ArAr80,80ArAr,1,1,, I127,127I,1,2,, Xe131,131Xe,1,3,, Xe134,134Xe,1,4,, Ba138,138Ba,1,5,, Pr141,aSMA,1,6,, Nd142,EGFR,1,7,, Nd143,p53,1,8,, Nd145,GFAP,1,9,, Nd148,Tenascin,1,10,, Eu151,CD31,1,11,, Eu153,CD44,1,12,, Gd155,Vimentin,1,13,, Gd156,Olig2,1,14,, Gd158,CD90,1,15,, Tb159,IDH1,1,16,, Gd160,PDGFRa,1,17,, Dy162,Nestin,1,18,, Dy164,mTOR,1,19,, Ho165,Musashi1,1,20,, Er166,H3K27me3,1,21,, Er168,Ki67,1,22,, Tm169,CollagenI,1,23,, Er170,H3G34R,1,24,, Yb171,CD248,1,25,, Yb172,Caspase3,1,26,, Yb174,BIIItubulin,1,27,, Lu175,H3K27M,1,28,, Yb176,MPP,1,29,, Os189,empty,1,30,, Ir191,DNA1,1,31,, Ir193,DNA2,1,32,, Pt195,ICSK1,1,33,, Pt196,ICSK2,1,34,, Pt198,ICSK3,1,35,, Pb208,208Pb,1,36,,