Hi, this is my first post, I apologize in advance if I make a mistake in the formatting or content…
Sample image and/or code
Example Images from Imagej ortho view
(note voxel dimensions are 0.108x0.108x1 microns).
I have a nuclei channel and a cell membrane channel. However there is a substantial amount of blur in the nuclei channel and I am having difficulty segmenting the nuclei into separate objects in 3D.
In the past I have used Huygens deconvolution software on laser scanning confocal images to correct for the PSF.
I am wondering if I can apply deconvolution to line scanning confocal images? I read a post on image.sc recommending uploading example images to a public forum to ask whether they think deconvolution could help me (here), so here I am!
Would this help to reduce the blur so that I can segment the nuclei?
If so, how would I calculate or measure the PSF of the INCELL 6000?
Are there any other techniques I could try?
Thank you for your help
- I would like to accurately segment individual nuclei in 3D from line-scanning confocal images.
- I am unable to accurately segment the nuclei into separate objects due to blur
- I have tried segmenting both in 2D and 3D using cell profiler identify primary objects and threshold modules, with watershed, respectively. I have also tried training an Ilastik model to identify out of focus and in focus nuclei pixels in z-stack layers. These attempts were unsuccessful.