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:

usage: main.py [-h] [-d DIRECTORY] [-s N] [-f N] [--dist] [-w WORKERS] [-j JOBS] [--keep KEEP] [--strategy STRATEGY] [--cluster CLUSTER] -i
               PATTERN -o DIRECTORY -c FILE -x FILE -t TEMP -e TEMP

optional arguments:
  -h, --help            show this help message and exit
  -d DIRECTORY, --debug DIRECTORY
                        path to the debug directory (enables debug mode)
  -s N, --start N       starting image (default: 0)
  -f N, --finish N      final image (defaults to until last image)
  --dist                use distance-based objective function
  -w WORKERS, --workers WORKERS
                        number of parallel workers (defaults to number of processors)
  -j JOBS, --jobs JOBS  number of jobs per frame (defaults to --workers/-w)
  --keep KEEP           number of top solutions kept (must be equal or less than --jobs/-j)
  --strategy STRATEGY   one of "best-wins", "worst-wins", "extreme-wins"
  --cluster CLUSTER     dask cluster address (defaults to local cluster)

required arguments:
  -i PATTERN, --input PATTERN
                        input filename pattern (e.g. "image%03d.png")
  -o DIRECTORY, --output DIRECTORY
                        path to the output directory
  -c FILE, --config FILE
                        path to the configuration file
  -x FILE, --initial FILE
                        path to the initial cell configuration
  -t TEMP, --temp TEMP  starting temperature for the simulated annealing
  -e TEMP, --endtemp TEMP
                        ending temperature for the simulated annealing
  -a AUTOTEMP --auto_temp 
                        enable auto-temperature schedule

Examples

python "./main.py" --start 0 --finish 13 --debug "./debug" --input "./input/frame%03d.png" --output "$TEST_DIR/output" --config "./config.json" --initial "./cells.0.csv" --temp 10 --endtemp 0.01