I have installed aics-segmentation and the machine learning section too, everything works great so far.
I have a question regarding the segmentation for laminb1 workflow :
It is design to work with 3d images (z stacks) but can I adapt it to work 2D (single z) since this is how we take the images for analysis in the lab.
So can I adapt /modify the workflow to work on single plane images ?
Next once I get the segmentation sorted , is it possible to get multiple single ROIs rather than a massive unique one ?
The idea is to use the single ROI (nucleus by nucleus) and apply it back on the original image to get the intensities of each lamin signal per nucleus .
In other words, I am looking to segment, make a mask and measure the intensities in the lamin channel for each single nucleus .
That way I can get all laminb1 intensities per nucleus per image.
Is that feasible, if so can you help me to design such a workflow ?
Thanks a lot!