matrixscreener 0.3.0

Features

• Access experiment as python object

• ImageJ stitching

• Communicate with microscope over CAM TCP/IP socket

Install

pip install matrixscreener

Examples

stitch experiment

import matrixscreener
# create short hand
Experiment = matrixscreener.experiment.Experiment

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

print(matrixscreener.imagej._bin) # default is for fiji on mac os x
matrixscreener.imagej._bin = '/path/to/imagej'

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

stitch specific well

from matrixscreener import experiment

# path should contain AditionalData and slide--S*
stitched_images = experiment.stitch('/path/to/well')

do stuff on images

from matrixscreener import experiment

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

# select specific parts
selected_wells = [well for well in scan.wells if 'U00' in well]
for well in selected_wells:
    do stuff...

def condition(path):
    x_above = experiment.attribute_as_int(path, 'X') > 1
    x_below = experiment.attribute_as_int(path, 'X') < 5
    return x_above and x_below

selected_fields = [field for field in scan.fields if condition(field)]
for field in selected_fields:
    do stuff..

subtract data

from matrixscreener.experiment import attribute_as_int

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

speak with microscope

from matrixscreener.cam import CAM

cam = CAM()   # initiate
cam.connect() # default localhost:8895

# command as tuples in list with keys and values
command = [('cmd', 'enableall'),
           ('value', 'true')]
response = cam.send(command)

# command as bytes string
command = b"/cmd:enableall /value:true"
bytes_sent = cam.socket.send(command)
response = cam.socket.recv(cam.buffer_size)

Dependencies

• ImageJ with Grid stitching plugin (fiji is recommended)

Develop

git clone https://github.com/arve0/matrixscreener.git
cd matrixscreener
# hack
./setup.py install

Testing

pip install tox
tox

API Reference

Use pydoc matrixscreener, pydoc matrixscreener.cam, pydoc matrixscreener.experiment, pydoc matrixscreener.imagej or read it online.