MIRROR pipeline¶
The mirror pipeline aims to register ssDNA image to GEM coordinate system with minimum registration error.
workflow¶
usage¶
main usage
MIRROR.py -h
Usage:
MIRROR.py action [options]
Actions:
prepare_registration_heatmap
prepare_registration_ssdna
second_registration
gem_to_gemc
gemc_to_h5ad
prepare_registration_heatmap¶
Usage : MIRROR.py prepare_registration_heatmap
argument |
description |
|---|---|
-g |
gem file |
-o |
output prefix |
-c |
chip715/chip500, default chip715 |
-e |
enhance by bin5, default not set |
-n |
yes/no draw trackline, default yes |
-x |
xmin, default None and calculate real xmin |
-y |
ymin, default None and calculate real ymin |
prepare_registration_ssdna¶
Usage : MIRROR.py prepare_registration_ssdna
argument |
description |
|---|---|
-d |
ssdna tif/png file |
-o |
output prefix |
-c |
chip500/chip715, default chip715 |
-w |
um per pixel in width, default 0.4803250 |
-h |
um per pixel in height, default 0.4802272 |
-f |
midfilt or not. default not set |
-m |
min_brightness, default 1 |
-M |
generate mask, default not set |
second_registration¶
Usage : MIRROR.py second_registration
argument |
description |
|---|---|
-H |
heatmap.trackline.tif/png |
-d |
ssDNA.trackline.tif/png |
-o |
output prefix |
-f |
Fujiyama output matrix, default None |
-t |
TrackEM output matrix, default None |
-a |
3*3 backward affine matrix, default none |
-c |
chip715/chip500, default chip500 |
-w |
um per pixel in width, default 0.5 |
-h |
um per pixel in height, default 0.5 |
-l |
S/M/L search area. default S |
-s |
thread number, default 8 |
-r |
roi json file, default none |
-F |
yes/no, default no. fake round2 |
- Note:
please only use one of ( -f , -a , -t ) .
Example of matrix¶
A 3*3 backward affine matrix¶
-f ‘[[0.033629421,0.983042659,-133.4590388],[-0.983042659,0.033629421,2262.081494],[0,0,1]]’
A 3*4 Fujiyama output matrix¶
-a ‘0.9789672225355872 -0.014001262294250694 0 0.014001262294229377 0.9789672225355872 0 0 0 0.9790673409653101 -49.386112981985995 -98.51787299912003 0’
A 2*3 TrackEM output matrix¶
-t ‘-0.010963829,-0.999939895,0.999939895,-0.010963829,-129.2603788,1664.628308’