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A Python module for loading lif file as numpy array

Project description

read_lif

Load 3D confocal images from lif files as numpy arrays.

The code was originally written by Mathieu Leocmach in package colloids.

Install

  • The most convenient way would be: pip install read_lif
  • You can also Include the file read_lif in your project directory

How to Use It

import read_lif

reader = read_lif.Reader('lif_file.lif')
series = reader.getSeries()
chosen = series[0]  # choose first image in the lif file
# get a numpy array corresponding to the 1st time point & 1st channel
# the shape is (z, y, x)
image = chosen.getFrame(T=0, channel=0)

Project details


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Files for read-lif, version 0.4.0
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