A Python module for loading lif file as numpy array
Project description
explore_lif
Load 3D confocal images from lif
files as numpy
arrays.
Install
- The most convenient way would be:
pip install -e .
from the directory where you have cloned or downloaded the code. - You can also Include the file
explore_lif
in your project directory
How to Use It
For 3D Image
from explore_lif import Reader
reader = 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 (x, y, z)
image = chosen.getXYZ(T=0, channel=0)
For 2D Image with Multiple Channels
from explore_lif import Reader
reader = 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
# the shape is (x, y, channel_number)
image = chosen.getXYC(T=0)
Project details
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