Phase-contrast-based Kinetic Analysis Algorithm for Amoebae (2022)
This is the image analysis algorithm used in the "Analysis of morphological changes in the nucleus and vacuoles of Acanthamoeba castellanii following medusavirus infection".

--- About analysis
The executable file of PKA3 is "./bin/pka3_2022.exe".
This should be executed on a windows computer with a 64-bit architecture.
You may need "Microsoft Visual C ++ Redistributable for Visual Studio 2015, 2017 and 2019" to execute this.

You can analyze the sample image with the command below.
PKA3_2022 -w 960 -h 720 -c 5 -i -o ../result -p ../sample/T%0/Image_T%0_Z%1_CH4.tif

The result is output to "./result/_average.csv".
3rd column : FIG 2A
4th column : FIG 2B, 2D
5th column : FIG 2C
7th column : FIG 3A
8th column : FIG 3B
10th column : FIG 3C, FIG 4A
11th column : FIG 3D, FIG 4B
14th column : FIG 5A, FIG 6A
15th column : FIG 5B, FIG 6B

--- Arguments
-w : The width of images. Must be a multiple of 4.
-h : The height of images. Must be a multiple of 4.
-c : The number of frames to analyze.
-i : Output result images.
-o : Directory path to output the results.
-p : The file path of the images to be analyzed.
-sc : The number of stacks in a frame.

--- Source code
The source code is contained in "./source".
It was developed using Visual Studio 2019.