cell segmentation scripts for large datasets in linux

[4ivage32]

Hi,

Thank you so much for developing this amazing tool! I've tested it on my confocal microscope data and was very impressed with the segmentation results.

I'm currently working with large-scale 3D datasets and would like to run your pipeline directly on Linux server for efficiency. Do you have any plans to provide a "one-click" batch processing script, so users can easily run it on folders of images from the command line like:

python 3DcellScope.py --in_dir input_path --out_dir output_path --channel 1 --prob_thres 0.5

This would be extremely helpful for high-throughput applications. Thanks again for your great work!

[quantacell]

Dear 4ivage32,
Thank you very much for your kind message and for your interest in our tool! We're glad to hear that it performed well on your confocal data.

At this stage, the provided script hasn't been formally validated on Linux systems, although in practice it may still work depending on the environment. A "one-click" batch version isn't included yet in the public release.

If you're working on high-throughput 3D datasets and would like to adapt the tool to your pipeline, feel free to reach out to us at contact_at_quantacell.com. We’d be happy to discuss how we can support your specific use case — including potential custom development if needed.

Best regards,
The QuantaCell Team