TrakEM2 pixel count

Hi guys,

looking for some help here and I guess this is the best place. :slight_smile:

I successfully managed to register a set of images in TrakEM2 with both automatic and manual corrections: really nice piece of software.

Problem is that I am interested in counting the average/sum of the pixel values in a ROI/AreaList and not just its area/perimeter/volume. Do you know if there is any chance to do this? Whenever I launch a measurement there is no information on the pixel count.

Alternatively I tried to export my grayscale images and perform this analysis with ImageJ afterwards but the only way to export figures is 8 bit while I have a 16 bit and then I lose the information that I have in the pixel values.

If anyone has a solution I would love if he or she could share it.
Thanks!

@albertcardona @axtimwalde Any suggestions?

There is a way, by exporting an ROI with arbitrary bit depth (e.g. 16-bit in your case) using a tiny script. Write to me in the ImageJ mailing list or to my email–I find the forum format difficult–and I’ll show you an example.

I encourage the communication to remain public, so that it can benefit others in the future. And if you switch the format (e.g., to the mailing list), then please cross-reference it with this thread.