leicaautomator API reference¶
leicaautomator package¶
# PLAN
scan whole slide with single regular matrix - input template name - output leicaexperiment.Experiment
find spots in whole slide - input leicaexperiment.Experiment - output list of dict
- position: spatial position
- well: well coordinate
for every spot - do a scan
- input - scan template name - x,y position in meters
- output - stitched image -> added to dict, image: imgdata
# Keep
- whole glass marked with well positions
- compressed spot scan
- stitched spots
- list_of_wells.json without imgdata
-
leicaautomator.
find_spots
(experiment)[source]¶ Finds spots and return position of them in a list.
- experiment : leicaexperiment.Experiment
- Matrix Screener experiment to search for spots. Its assumed that the experiment contain a single well. If it contain several wells, only the first well will be searched for spots.
- list of regions from skimage.measure.regionprops
Regions have these extra attributes:
real_x
:x
in meters.real_y
:y
in meters.x
,y
,x_end
,y_end
: same asbbox
.well_x
: well x coordinate, from 0.well_y
: well y coordinate, from 0.
Submodules¶
leicaautomator.automator module¶
# PLAN
scan whole slide with single regular matrix - input template name - output leicaexperiment.Experiment
find spots in whole slide - input leicaexperiment.Experiment - output list of dict
- position: spatial position
- well: well coordinate
for every spot - do a scan
- input - scan template name - x,y position in meters
- output - stitched image -> added to dict, image: imgdata
# Keep
- whole glass marked with well positions
- compressed spot scan
- stitched spots
- list_of_wells.json without imgdata
-
leicaautomator.automator.
find_spots
(experiment)[source]¶ Finds spots and return position of them in a list.
- experiment : leicaexperiment.Experiment
- Matrix Screener experiment to search for spots. Its assumed that the experiment contain a single well. If it contain several wells, only the first well will be searched for spots.
- list of regions from skimage.measure.regionprops
Regions have these extra attributes:
real_x
:x
in meters.real_y
:y
in meters.x
,y
,x_end
,y_end
: same asbbox
.well_x
: well x coordinate, from 0.well_y
: well y coordinate, from 0.
leicaautomator.viewer module¶
scikit-image viewer plugins and widgets.