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Cross Comparison Representation Learning for Semi-supervised Segmentation of Cellular Nuclei in Immunofluorescence Staining

Installation

  • Install Pytorch 1.11.0 and CUDA 10.0
  • Clone this repo
git clone https://github.com/rxy1234/CCRL
cd CLSD

Data Preparation

  • Download CRAG dataset
  • Download ISC dataset
  • Put the data under ./data/
  • Divide the dataset into six folders myTest_Data myTest_Label myTraining_Data myTraining_Label myValid_Data myValid_Label
  • Fill the folder myTest_Label with images with pixel values of all 0 corresponding to the folder myTest_Data

Train

  • Open ema_train.txt in the folder scripts
  • Copy content after modifying parameters
  • Open the terminal and cd 'the path of the current project'
  • Paste the copied operation command and run it

Evaluate

  • Download Test dataset
  • Put the test data under ./data/
  • Download Parameter
  • Put the parameter under ./exp/
  • Open ema_test.txt in the folder scripts
  • Copy content after modifying parameters
  • Open the terminal and cd 'the path of the current project'
  • Paste the copied operation command and run it

Acknowledgement

Some code is reused from the Pytorch implementation of mean teacher.

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