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Cell-ACDC in OOD

Cell-ACDC is a GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data.

Getting Started​

You can run Cell-ACDC in OOD by going to the URL ood.hpc.nyu.edu in your browser and selecting Cell-ACDC from the Interactive Apps pull-down menu at the top of the page. Once you've used it and other interactive apps they'll show up on your home screen under the Recently Used Apps header.

note

Be aware that when you start from Recently Used Apps it will start with the same configuration that you used previously. If you'd like to configure your Cell-ACDC session differently, you'll need to select it from the menu.

Configuration​

You can select the number of cores, amount of memory, and number of hours.

OOD Cell-ACDC Configuration

Cell-ACDC running in OOD​

After you hit the Launch button you'll have to wait for the scheduler to find node(s) for you to run on: OOD Cell-ACDC in queue

Then you'll have a short wait for the Cell-ACDC itself to start up.
Once that happens you'll get one last page that will give you links to:

  • open a terminal window on the compute node your Cell-ACDC session is running on
  • go to the directory associated with your Session ID that stores output, config and other related files for your session
  • make changes to compression and image qualtiy
  • get a link that you can share that will allow others to view your Cell-ACDC session

Pre-launch Cell-ACDC OOD

Please click the Launch Cell-ACDC button and a Cell-ACDC window will open.