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.

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

Version History

Version 1 (earliest) Created 17th Sep 2024 at 14:54 by yi.sun@embl.de

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Created: 17th Sep 2024 at 14:54

Last updated: 18th Sep 2024 at 08:29

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