Nuclei segmentation and shape measurement
Version 1

Workflow Type: Galaxy

Stable

Detecting a set of objects in an image, counting them and measuring certain characteristics about their morphology is probably the most frequently occurring task in bioimage analysis. Depending on the image, even this task could become quite challenging and the workflow could become quite complex. Here we start with a relatively simple image where combining a minimal set of image analysis components into a simple workflow does the job.

SEEK ID: https://dev.workflowhub.eu/workflows/1364?version=1

Steps

ID	Name	Description
0	Threshold image	toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3
1	Convert binary image to label map	toolshed.g2.bx.psu.edu/repos/imgteam/binary2labelimage/ip_binary_to_labelimage/0.5+galaxy0
2	Colorize label map	toolshed.g2.bx.psu.edu/repos/imgteam/colorize_labels/colorize_labels/3.2.1+galaxy2
3	Extract image features	toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0

Outputs

ID	Name	Description	Type
binary_image	#main/binary_image	n/a	File
colorized_labelimage	#main/colorized_labelimage	n/a	File
labelled_image	#main/labelled_image	n/a	File
measurements	#main/measurements	n/a	File