fluorescence-nuclei-segmentation-and-counting/main
Version 1

Workflow Type: Galaxy

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Inputs

ID Name Description Type
input_image #main/input_image The fluorescence microscopy images to be segmented. Must be the single image channel, which contains the cell nuclei.
  • File

Steps

ID Name Description
1 Filter 2D image toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/0.0.3-3
2 Perform histogram equalization toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.0.1-2
3 Threshold image toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.0.5-2
4 Convert image format toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy2
5 Convert binary image to label map toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0
6 Overlay images toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy0
7 Count objects in label map toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2

Outputs

ID Name Description Type
label_image #main/label_image n/a
  • File
objects_count #main/objects_count n/a
  • File
overlay_image #main/overlay_image n/a
  • File

Version History

v0.1 (earliest) Created 1st Mar 2024 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 f66ee02
help Creators and Submitter
Creator
  • Leonid Kostrykin
Submitter
License
Activity

Views: 440

Created: 1st Mar 2024 at 03:01

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