leicaexperiment 0.2.0

Read, stitch and compress Leica LAS Matrix Screener experiments

Overview

This is a python module for interfacing with Leica LAS AF/X Matrix Screener experiments.

The module can be used to:

• stitch wells from an experiment exported with the LAS AF Data Exporter

• batch compress images lossless

• programmatically select slides/wells/fields/images given by attributes like

  • slide (S)

  • well position (U, V)

  • field position (X, Y)

  • z-stack position (Z)

  • channel (C)

Features

• Access experiment as a python object

• Compress to PNGs without loosing precision, metadata or colormap

• ImageJ stitching (Fiji is installed via fijibin)

Installation

Install using pip…

pip install leicaexperiment

Examples

stitch experiment

from leicaexperiment import Experiment

# path should contain AditionalData and slide--S*
experiment = Experiment('path/to/experiment')

# if path is omitted, experiment path is used for output files
stitched_images = experiment.stitch('/path/to/output/files/')

# get information about placement of images in the stitch
xs, ys, attrs = experiment.stitch_coordinates(well_x=0, well_y=0)

stitch specific well

from leicaexperiment import stitch

stitched_images = stitch('/path/to/well')

do stuff on all images

from leicaexperiment import Experiment

experiment = Experiment('path/to/experiment--')

for image in experiment.images:
    do stuff...

do stuff on specific wells/fields

from leicaexperiment import Experiment
from PIL import Image

experiment = Experiment('path/to/experiment--')

# on images in well --U00--V00
for well in experiment.well_images(0, 0):
    do stuff...

# rotate top left image in first row
rows = experiment.well_rows
for r in rows:
    img_path = experiment.image(r, 0, 0, 0)
    img = Image.open(img_path)
    img = img.rotate(90)
    img.save(img_path)

subtract attributes from file names

from leicaexperiment import attribute

# get all channels
channels = [attribute(image, 'C') for image in experiment.images]
min_ch, max_ch = min(channels), max(channels)

batch lossless compress of experiment

from leicaexperiment import Experiment

e = Experiment('/path/to/experiment')
pngs = e.compress()
print(pngs)

API reference

API reference is at http://leicaexperiment.rtfd.org.

Development

Install dependencies and link development version of leicaexperiment to pip:

git clone https://github.com/arve0/leicaexperiment
cd leicaexperiment
pip install -r requirements.txt

run test

pip install tox
tox

extra output, jump into pdb upon error

DEBUG=leicaexperiment tox -- --pdb -s

build api reference

pip install -r docs/requirements.txt
make docs