Questions about tutorial: `3D Noise Nuclei segmentation`

[d33bs]

Hello, thanks for providing and maintaining this tutorial repo! I was looking for a good open source example of 3D image processing in CellProfiler and came across the 3D Noise Nuclei segmentation tutorial here.

As a background, this tutorial dataset includes 4 3d images which are of shape: (T=1, C=1, Z=100, Y=258, X=258). Each image seems to contain about 5 objects. A cppipe file is included which can help process these images. I was able to run the pipeline to successfully create profiles using CellProfiler v4.2.8.

Data differences

I noticed that after running the cppipe on the source images I ended up with a CSV called MyExpt_RealsizeNuclei.csv which appeared to have nuclei features included. Based on some work with 2d data within CellProfiler I was somewhat surprised to find this file contained 400 rows (seemingly in alignment with z-slices but not total objects). See here: MyExpt_RealsizeNuclei.csv.

In making some slight changes to the cppipe file (see here) I was able to reduce this down to 20 rows (in alignment with the actual objects from the images - 5 per image). See here: MyExpt_RealsizeNuclei.csv.

Note: It looked like the tutorial cppipe file was created using CellProfiler v4.2.1, so there could be some differences in processing, but I wasn't sure exactly.

Question: what should we ideally expect for data output from the pipeline for this tutorial, given the data and goals? Mostly I wonder: should we expect 400 records of objects (1 per z-slice) or 20 records of objects (1 per actual object from the images).

Citations

How can we cite this repository and the related tutorial data I mention above? I didn't see any specifics on this but wanted to be sure to credit anyone involved.

Thanks for any help you can offer on both of these! And again, appreciate the effort which goes into maintaining this project - it's great!