imageProcessing package

Submodules

imageProcessing.alignImages module

imageProcessing.alignImages3D module

imageProcessing.imageProcessing module

Classes for common image processing

class imageProcessing.imageProcessing.Image(current_log=None)

Bases: object

get_image_filename(root_folder, tag)
load_image(file_name)
load_image_2d(file_name, master_folder, tag='_2d')
save_image_2d(root_folder, tag='_2d')
show_image(show=False, size=(10, 10), output_name='tmp.png', save=True, normalization='stretch')
imageProcessing.imageProcessing.image_adjust(image, lower_threshold=0.3, higher_threshold=0.9999)
Adjust intensity levels:

  • rescales exposures

  • gets histogram of pixel intensities to define cutoffs

  • applies thresholds

Parameters

  • image (numpy array) – input 3D image.

  • lower_threshold (float, optional) – lower threshold for adjusting image levels. The default is 0.3.

  • higher_threshold (float, optional) – higher threshold for adjusting image levels.. The default is 0.9999.

Returns

  • image1 (numpy array) – adjusted 3D image.

  • hist1_before (numpy array) – histogram of pixel intensities before adjusting levels.

  • hist1 (numpy array) – histogram of pixel intensities after adjusting levels.

  • lower_cutoff (float) – lower cutoff used for thresholding.

  • higher_cutoff (float) – higher cutoff used for thresholding.

imageProcessing.imageProcessing.preprocess_3d_image(x, lower_threshold, higher_threshold, parallel_execution=True)
3D stack pre-processing:

  • rescales intensities to 0->1

  • removes inhomogeneous background plane by plane

  • adjusts image levels by thresholding

Parameters

  • x (numpy array) – 3D image.

  • lower_threshold (float) – lower threshold for adjusting image levels.

  • higher_threshold (float) – higher threshold for adjusting image levels..

Returns

image – pre-processed 3D image.

Return type

numpy array

imageProcessing.imageProcessing.reassemble_3d_image(client, futures, output_shape)

waits for futures to arrive collects them into a results list reassembles 3D image plane by plane

Parameters

  • client (dask CLient()) – result of get_client()

  • futures ([]) – list of futures

  • output_shape (tuple) – result of image.shape

Returns

output – contains reassembled 3D image.

Return type

numpy array

imageProcessing.imageProcessing.scatter_3d_image(image)

splits 3D image plane by plane and scatteres them to a cluster

Parameters

image (numpy array) – 3D image.

Returns

image_list_scattered – scattered image.

Return type

List, dict, iterator, or queue of futures matching the type of input.

imageProcessing.makeProjections module

imageProcessing.segmentMasks module

imageProcessing.segmentMasks3D module

imageProcessing.segmentSources3D module

Module contents

Created on Wed Aug 12 15:59:09 2020

@author: marcnol

The pyHi-M.projections package includes functions to produce 2D projections from 3d images