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

SEEK ID: https://workflowhub.eu/workflows/771?version=1

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

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