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Tools for light microscopy based bioreactor control

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lmcontrol

Tools for light microscopy based bioreactor control

Installation

The following commands will install the code in this repository in such a way that will allow one to use the tools provided by said code. With that said, the provided sequence of commands may not suit your specific needs. As this repository follows PEP 517 style packaging, there are many ways to install the software, so please use discretion and adapt as necessary.

git clone [email protected]:lbl-cbg/lmcontrol.git
cd lmcontrol
pip install -r requirements.txt
pip install .

Commands

Segmentation

  • lmcontrol crop - Crop light microscopy images to bounding box around single cell.
  • lmcontrol prep-viz - Prepare package for running interactive visualizer. See emb-viz command for more details.
  • lmcontrol emb-viz - Launch interactive visualizer for exploring segmented and cropped images.

Self-supervised Learning

  • lmcontrol train-byol - Train a model with BYOL
  • lmcontrol infer-byol - Create embeddings with BYOL-trained model

notebooks

  • Segment.ipynb - This notebook describes how image segmentation was done.

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Tools for light microscopy based bioreactor control

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