counts of cells in z-stack image

[albot]

Hi All,

I was wondering if there is a script available in Omero to count a number of cells in a z-stack image in a way that you can set a minimum volume to make sure that it counts cells?
I used to use Imaris Version 6.1.0 software (Bitplane) for this, but since our licence expired, i want to know if i can find an alternative.

thanks a lot.

Cheers
Alex

[wmoore]

Hi Alex,

I don't know of anything offhand, but if something like this works for you
http://stackoverflow.com/questions/5298 ... ing-python
and you can get scipy installed, then it should be trivial to include that kind of analysis in an OMERO.script.

If all you need is the number of cells counted, then it is easy to return the value or add it as an annotation to the image.
You could even try to save the resulting image back to OMERO.

I guess that other alternatives would be to use something like ImageJ to do the analysis and run ImageJ commands from a script using https://github.com/imagej/imagej-omero, but this is probably not ready for production yet.

If you can find some scipy commands that do what you want, I can help you to include that in an OMERO.script.

Will.