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 as bbox.
  • 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 as bbox.
  • well_x : well x coordinate, from 0.
  • well_y : well y coordinate, from 0.
leicaautomator.automator.get_x_median(regions, x)[source]

Get median position of given regions.

regions : list of RegionProperties
List of regions with region.real_x and region.real_y set.
x : int
Which x well position to get median for.
leicaautomator.automator.get_y_median(regions, y)[source]

Get median position of given regions.

regions : list of RegionProperties
List of regions with region.real_x and region.real_y set.
y : int
Which y well position to get median for.

leicaautomator.utils module

leicaautomator.utils.flatten(iterable)[source]
leicaautomator.utils.save_regions(regions, filename)[source]

Save regions as compressed (gzip) pickle.

leicaautomator.viewer module

scikit-image viewer plugins and widgets.

leicaautomator.viewer.create_polygon(r)[source]