Oral Cell Data Preparation

Dependencies

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

Usage

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