Sample image and/or code
I have been following smFISH analysis outline using FISHquant in Matlab. I am attempting to perform robust segmentation of cell outlines. I have been following this protocol: file:///C:/Users/hhrnc/Downloads/FISH_QUANT__Tutorials%20(2).pdf
HOWEVER, things delineate in CellProfiler because I had to make my own pipeline which is pictured above to get ‘masks’ to export to Matlab to use as an outline in FISHquant. The reason I had to make my own pipeline is because I get the following error message when I try to use to pre-designed pipeline I get a pipeline version mismatch error message (pictured above).
When I try to use the masks created in CellProfiler in Matlab I get the error message that my tiffs are “not a mask for cells”. Please help. I have tried for so long. I have updated my Java and and am using the most recent version of CellProfiler (4.0).
I want to create automatic cell outlines for smFISH analysis in FISH-Quant.
I am new to CellProfiler and FISH-Quant.