Hello Allen Cell Segmentation Developers,
I have read “Robust integrated intracellular organization of the human iPS cell” and “The Allen Cell and Structure Segmenter”. I am trying to create a 3D single cell image data set, which includes the cell membrane and nucleus, utilizing the classic work flow and the tools in Napari. I have been able to segment the cell membrane and the nucleus with different classic workflows, after the previous help you provided. The problem I am now having is that I cannot access certain repositories to run the segmenter_model_zoo.
From what I read in the “Robust” paper, this is the path I should take. However, I am not sure if this is correct. If you could direct me to the correct method / code to create single cell 3D images from an image that has multiple cells in the field of view I would greatly appreciate it.
I also have one more question. In the classic segmenter there is a workflow named cardio_fbl_100x. I have checked each of the options in Napari and I am unable to find this workflow. The reason I ask is that out of all of the workflows, this classic workflow works the best on segmenting the cell membrane in our images and I would like to use it for 3D segmentation as well.
Thank you for your assistance!