dcimg

This module provides the DCIMGFile class for accessing Hamamatsu DCIMG files.

Installation

pip install dcimg

Documentation

The DCIMGFile class provides an interface for reading 3D Hamamatsu DCIMG files.

Usage is pretty straightforward. First of all, create a DCIMGFile object:

>>> my_file = DCIMGFile('input_file.dcimg')
>>> my_file
    <DCIMGFile shape=2450x2048x2048 dtype=<class 'numpy.uint16'> file_name=input_file.dcimg>

Image data can then be accessed using NumPy's basic indexing:

>>> my_file[-10, :5, :5]
array([[101, 104, 100,  99,  89],
       [103, 102, 103,  99, 102],
       [101, 104,  99, 108,  98],
       [102, 111,  99, 111,  95],
       [103,  98,  99, 104, 106]], dtype=uint16)

Other convenience methods for accessing image data are: zslice, zslice_idx, frame and whole.

DCIMGFile supports context managers:

with DCIMGFile('input_file.dcimg') as f:
     a = f[800, ...]

To access the whole file as a Dask Array, use as_dask_array():

my_file = DCIMGFile('input_file.dcimg')
da = my_file.as_dask_array()

For further details refer to: https://lens-biophotonics.github.io/dcimg/