This is my first post to this community. I ask similar question to stackoverflow and someone refer this to me and I land up to this community. After reading some post, I felt this is the right platform to ask and take suggestion from the experts.
I am new to image processing of biomedical images. I have DAPI stained of nuclei of some tissue. My task it to segment nuclei and find the properties of different nuclei. I have few questions.
- My image dimension is 978x6048x1965(zyx) and size of around ~10 Gb. It is unable to load in ilastik. After resizing the image I can able to upload in Ilastik and do the segment but is it right method to do?
- For this image
Is it possible to do the segment of the nuclei because nuclei are very dense or do I need to apply any filter before segmenting?
- Just want to confirm that I am doing the right steps or not.
I select features and class labels of nuclei at z=200 plane. Then I did the live prediction of entire x y pixels of z=200 plane and re do the process with assignment of more corrected labels. Now I have to get probabilities of the segmented nuclei for entire stack of z =1:400
So, i load whole stack again in batch mode and run & save.
Are these steps right?
- Ilastik returns probabilities in zyxc format. Here c has two channel. First channel refers background pb 0 and object pb 1. Second channel refers background pb 1 and object pb 0.
So, I need to use only one channel for further analysis. Am I right?
If I am wrong, please correct me. Thanks for your help.