OralCellDataPreparation

Oral Cell Data Preparation

Dependencies

• NDPITools (choose NDPITools software version, independent of ImageJ)
• Install MATLAB Engine API for Python
• Other packages for python

Usage

1. Clone this repository to the directory of the NDPI files.

2. There are two options for this step:

   1. Edit the path for inputFolder and outputFolder in particle_analysis_fixedDirectory.ijm :

      inputFolder="/PATH_TO/OralCellDataPreparation/PredMasks/";
      outputFolder="/PATH_TO/OralCellDataPreparation/CSVResults/";
      

   2. Or alternatively, replace

      ImageJ --headless -macro particle_analysis_fixedDirectory.ijm

      with

      ImageJ -macro particle_analysis.ijm

      in data_preparation.sh. Then the path for inputFolder and outputFolder will need to be selected when prompted.

3. Run

   cd OralCellDataPreparation
   ./data_preparation.sh

   The focused patches will be generated in /PATH_TO/OralCellDataPreparation/Patches/Z_focused/.

   Or replace

   nohup python3 select_focus.py >./nohup.out 2>./nohup.err &

   with

   ./select_focus_parallel.sh N

   to run in parallel, where input argument N is the number of processes.

   The progress bar is redirected in /PATH_TO/OralCellDataPreparation/debugging/*.err, together with the error messages.

Known Problems

• There might be some "imread error". This is due to trying to read some corrupted images. They are handled by being ignored.