multiScaleAnalysis.SegmentationLowres package

Submodules

multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched module

class multiScaleAnalysis.SegmentationLowres.segment_lowres_3d_stitched.segment_macrophage_lowres_class[source]

Bases: object

This class gathers all functions to segment the macrophage and cancer cells of the low-resolution data.

__init__()[source]

Initialization, including GPU initalization and parameter

iterate_throughfolder(parentfolder, resultsfolder, channellist)[source]

Iterate through a folder with rawdata that should be segmented, generate filenames and calls the segmentation folders.

Parameters:

  • parentfolder – folder through which to iterate

  • resultsfolder – folder where to save the outcome

  • channellist – iterate through channels

open_image(imagename)[source]

Open image.

Parameters:

imagename – file path to current image

segment_cancercells(savepath, background_substracted_path='path', savepath_xlsx='pathxlsx')[source]

Segment cancer cells in the low-resolution image and save the resulting segmentation and segmentation statistics.

Parameters:

  • savepath – path to save segmentation outcome

  • background_substracted_path – path to save background substracted image (optional)

  • savepath_xlsx – path to save segmentation statistics

segment_macrophage(savepath, background_substracted_path='path', savepath_xlsx='pathxlsx')[source]

Segment macrophages in the low-resolution image and save the resulting segmentation and segmentation statistics.

Parameters:

  • savepath – path to save segmentation outcome

  • background_substracted_path – path to save background substracted image (optional)

  • savepath_xlsx – path to save segmentation statistics

Module contents