PENGUINLIONG / CellUniverse

Cell Universe

Tracks the movement of cells from a video source.

Initial Properties File

This is an example initial properties file:

# Initial property file (line commented out)

0.33   	  	   	#dt, or the number of hours per frame
26    			#init_length of bacteria
6     			#init_width of bacteria
3     			#max speed
0.3141592653589793	#max spin
20			#number of ideal universes
3			#max x motion
3			#max y motion
7			#max x resolution
7			#max y resolution
0.3141592653589793	#max rotation
21			#max rotation resolution
0			#minimum height increase
3			#maximum height increase
4			#height increase resolution
31			#maximum length of single bacteria before splitting
13			#minimum length of any bacteria
0.25			#beginning of split ratio
0.75			#end of split ratio
20			#split ratio resolution
#NOTE: The program will ignore comments

pos:x   pos:y   length  rotation
160     105     20      1.605
156     125     17      1.997
165     130     14      1.997
170     113     15      1.605

You can start with one or more cell properties. The rotation is specified in radians.

Also, you may specify the names manually:

# Initial property file

0.33
26
6
3
0.3141592653589793
20
3
3
7
7
0.3141592653589793
21
0
3
4
31
13
0.25
0.75
20

name    pos:x   pos:y   length  rotation
"00"    160     105     20      1.605
"01"    156     125     17      1.997
"10"    165     130     14      1.997
"11"    170     113     15      1.605

Frames

Images must all be placed in a directory. The default is ./frames/ directory, but you can change the name as long as you input the directory in the command line. The names of the images must match 0.png, 1.png, 2.png, and so on.

Usage

Command line help:

$ python celluniverse.py --help
usage: celluniverse.py [-h] [-f DIR] [-v] [-s FRAME] [-p COUNT] [-o OUTDIR] initial

Cell-Universe Cell Tracker.

positional arguments:
  initial               initial properties file ('example.init.txt')

optional arguments:
  -h, --help            show this help message and exit
  -f DIR, --frames DIR
			specify directory of all the frames (default: frames/)
  -v, --version         show program's version number and exit
  -s FRAME, --start FRAME
                        start from specific frame (default: 0)
  -p COUNT, --processes COUNT
                        number of concurrent processes to run (default: 4)
  -o OUTDIR, --output OUTDIR
			specify output directory name (default: Output/)

Examples

python celluniverse.py --frames frames/ --processes 2 --output Output/ example1.init.txt