These are the files related to PKA3, the analysis program used in our paper "Kinetic analysis of Acanthamoeba castellanii infected with giant viruses quantitatively revealed process of morphological and behavioral changes in host cells".
The source code, executable file, sample, and this readme file can be obtained from the following.
https://pkaaa2021.z11.web.core.windows.net/pka3.zip

--- About Analysis
The executable file of PKA3 is "./bin/pea3.exe".
This should be executed on a windows computer with a 64-bit architecture with a GPU.
You may need "Microsoft Visual C ++ Redistributable for Visual Studio 2015, 2017 and 2019" to execute this.

If you execute the following command at the command prompt where the current directory is "./bin", the sample images (./sample) will be analyzed.

pea3 -w 960 -h 720 -count 10 -size 320 -threshold 8 -image -source ../sample/image%04d.tif -output ../result

The result is output to "./result".
The 5th, 7th and 15th columns of "./result/_average.csv" are the values related to FIG 2.
The 9th, 12th and 4th columns of "./result/_average.csv" are the values related to FIG 3, 6.
The 18th and 27th columns of "./result/_cell.csv" are the values related to FIG 4.
The 7th and 8th columns of "./result/_cell.csv" are the values related to FIG 5.
The 4th, 6th and 30th columns of "./result/_cell.csv" are the values related to FIG 7, 8, 9.

The arguments of pea3.exe are as follows.
-x 0 : The X coordinate at the top left of the analysis area. 
-y 0 : The Y coordinate at the top left of the analysis area.
-w 960 : The width of the analysis area. Must be a multiple of 4.
-h 720 : The height of the analysis area. Must be a multiple of 4.
-count 10 : The number of images to analyze.
-size 320 : The size of the largest small particle.
-threshold 8 : The smaller the value, the finer the particles will be analyzed, which can be noisy.
-image : Output the image of the analysis result.
-id : Shows the particle ID in the output image (-image is required).
-voronoi : Output the image of Delaunay diagram.
-source ../sample/image%04d.tif : The file path of the images to be analyzed. "%04d" is converted to a 4-digit number starting with 0001.
-output ../result : Directory path to output the analysis result.

--- About Source Code
The source code is contained in "./source".
It was developed using Visual Studio 2019.
To build it, you need Intel Software Development Tools for OpenCL.

--- About Data
The microscopic images taken in this paper can be obtained from the following (each is 1GB or more).
https://pkaaa2021.z11.web.core.windows.net/kyoto_moi_0.zip
https://pkaaa2021.z11.web.core.windows.net/kyoto_moi_1.zip
https://pkaaa2021.z11.web.core.windows.net/kyoto_moi_10.zip
https://pkaaa2021.z11.web.core.windows.net/kyoto_moi_100.zip
https://pkaaa2021.z11.web.core.windows.net/mimi_moi_0.zip
https://pkaaa2021.z11.web.core.windows.net/mimi_moi_1.zip
https://pkaaa2021.z11.web.core.windows.net/mimi_moi_10.zip
https://pkaaa2021.z11.web.core.windows.net/mimi_moi_100.zip
https://pkaaa2021.z11.web.core.windows.net/medusa_moi_0.zip
https://pkaaa2021.z11.web.core.windows.net/medusa_moi_1.zip
https://pkaaa2021.z11.web.core.windows.net/medusa_moi_10.zip
https://pkaaa2021.z11.web.core.windows.net/medusa_moi_100.zip
https://pkaaa2021.z11.web.core.windows.net/pandora_moi_0.zip
https://pkaaa2021.z11.web.core.windows.net/pandora_moi_1.zip
https://pkaaa2021.z11.web.core.windows.net/pandora_moi_10.zip
https://pkaaa2021.z11.web.core.windows.net/pandora_moi_100.zip

The analysis results of these images can be obtained from the following.
https://pkaaa2021.z11.web.core.windows.net/result.zip