ndbioimage 2022.7.1

Bio image reading, metadata and some affine registration.

ndbioimage

Exposes (bio) images as a numpy ndarray like object, but without loading the whole image into memory, reading from the file only when needed. Some metadata is read and exposed as attributes to the Imread object (TODO: structure data in OME format). Additionally, it can automatically calculate an affine transform that corrects for chromatic abberrations etc. and apply it on the fly to the image.

Currently supports imagej tif files, czi files, micromanager tif sequences and anything bioformats can handle.

Installation

pip install ndbioimage@git+https://github.com/wimpomp/ndbioimage.git

With bioformats (if java is properly installed)

pip install ndbioimage[bioformats]@git+https://github.com/wimpomp/ndbioimage.git

With affine transforms (only for python 3.8, 3.9 and 3.10)

pip install ndbioimage[transforms]@git+https://github.com/wimpomp/ndbioimage.git

Usage

• Reading an image file and plotting the frame at channel=2, time=1

  import matplotlib.pyplot as plt from ndbioimage import imread with imread('image_file.tif', axes='ctxy', dtype=int) as im: plt.imshow(im[2, 1])

• Showing some image metadata

  from ndbioimage import imread from pprint import pprint with imread('image_file.tif') as im: pprint(im)

• Slicing the image without loading the image into memory

  from ndbioimage import imread with imread('image_file.tif', axes='cztxy') as im: sliced_im = im[1, :, :, 100:200, 100:200]

sliced_im is an instance of imread which will load any image data from file only when needed

• Converting (part) of the image to a numpy ndarray

  from ndbioimage import imread import numpy as np with imread('image_file.tif', axes='cztxy') as im: array = np.asarray(im[0, 0])

Adding more formats

Readers for image formats subclass Imread. When an image reader is imported, Imread will automatically recognize it and use it to open the appropriate file format. Image readers subclass Imread and are required to implement the following methods:

• staticmethod _can_open(path): return True if path can be opened by this reader
• __metadata__(self): reads metadata from file and adds them to self as attributes,
  • the shape of the data in the file needs to be set as self.shape = (X, Y, C, Z, T)
  • other attributes like pxsize, acquisitiontime and title can be set here as well
• __frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file

Optional methods:

• open(self): maybe open some file
• close(self): close any file handles

Optional fields:

• priority (int): Imread will try readers with a lower number first, default: 99
• do_not_pickle (strings): any attributes that should not be included when the object is pickled, for example: any file handles

TODO

• structure the metadata in OME format tree
• re-implement transforms