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angelolab / ark-analysis

Integrated pipeline for multiplexed image analysis
https://ark-analysis.readthedocs.io/en/latest/
MIT License
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Local Deepcell or Cellpose server for larger tile segmentation #1035

Open jamesMo84 opened 1 year ago

jamesMo84 commented 1 year ago

Hi, Great package, I've started applying the pipeline to TMA cores but am running into the issue with Deepcell Kiosk max tile size of 2048x2048. Is there scope to specify a local segmentation server (DeepCell or Cellpose) into ark.utils.deepcell_service_utils to overcome this tile size limit? how does one find and call the host name from alocal Deepcell server installed as per https://github.com/vanvalenlab/deepcell-tf

ngreenwald commented 1 year ago

Hi @jamesMo84, There's currently not a way baked into the notebook to rely on a local installation of Mesmer/Cellpose, mostly because it would significantly increase the complexity of the dependencies. However, if you already have a local segmentation solution set up to process large images, you'd just need to name them appropriately so that the rest of the notebook could read them in and process them. You can then skip the cell that formats and uploads for the deepcell server, and do the process yourself.

There's also a dedicated repo with a containerized version: https://github.com/vanvalenlab/deepcell-applications

Samlee-xx commented 1 year ago

Hi, @jamesMo84 Have you solved your problem? I encounter the same problem,too. I will appreciate if you can share some experience. Thanks a lot !