Detect blastema by pigment difference¶
Workflow¶
Example¶
raw photo¶
2D mapping photo of 3D atlas¶
align photo and detect wound mask¶
assign region to each cell¶
python3 BlastemaByWound_v2.py
arguments |
description |
|---|---|
-p |
prefix |
-o |
output prefix, default output |
-e |
exponential number, default 2 |
–only_wound |
yes/no, default no |
-l |
left wound left extern distance, default 20 |
–lr |
left wound right extern distance, default 20 |
–rl |
right wound left extern distance, default 20 |
–rr |
right wound right extern distance, default 20 |
Note: the unit of distance is 3 micron, so the default 10 refer to 60 microns.
Example :
example 01: python3 BlastemaByWound.py -p 12hpa1
example 02: python3 BlastemaByWound.py -p WT -o test_WT
example 02: python3 BlastemaByWound.py -p 5dpa1 -o test_5dpa1 -e 3
example 03: python3 BlastemaByWound.py -p 3dpa1 -o test_3dpa1_lr15 –lr 15
Output label :
1 – [red] left blastema
2 – [green] left margin of left wound
3 – [magenta] right margin of left wound
4 – [yellow] body
5 – [white] left margin of right wound
6 – [cyan] right margin of right wound
7 – [orange] right blastema
Output label in only_wound mode:
3 – [magenta] left wound region, similar to 1+2+3 in blastema mode
4 – [yellow] body
5 – [white] right wound region, similar to 5+6+7 in blastema mode
final region image¶
