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jo-mueller / FociCounter

Performs auto-segmentation of cell nuclei. User then picks viable cells manually and the number of gH2AX foci are counted and their sizes measured.
MIT License
3 stars 2 forks source link

save cell-wise images #12

Open Franzi-ba opened 2 years ago

Franzi-ba commented 2 years ago

save cell-wise images does not work. The exported images are just black

jo-mueller commented 2 years ago

Hi @Franzi-ba ,

thanks for reporting this! Just to clarify - were cells visibly identified by StarDist in some of the first processing steps? If you set the script into batch mode (there is a checkbox in the user interface), it should stop and ask you if you agree with the selection of cells to be analyzed.

Other than that, I think the exported cell images should be stacks showing the original stainings (DAPI + gH2AX) as well as the generated binary masks. Have you checked whether the color limits were set appropriately when you open the exported images? Thanks for the feedback!

Franzi-ba commented 2 years ago

yes, StarDist worked.

I realised that I opened the images with the wrong program. It reduced the TIF to its black background. Nevertheless, only the foci is in one of the layers. It seems like, the outline of the cell is missing.

jo-mueller commented 2 years ago

Hi @Franzi-ba ,

could you send me an example dataset so I could try and reproduce the problem? You can mail it to johannes_richard.mueller@tu-dr***.de. Thanks in advance!