Segmentation_Values_Testing
1.0

Workflow Type: Galaxy

Workflow to assess nuclei segmentation by applying different Gaussian filtering values during image pre-processing.

Associated Tutorial

This workflows is part of the tutorial Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy, available in the GTN

Features

Thanks to...

Workflow Author(s): Riccardo Massei

Tutorial Author(s): Riccardo Massei

Tutorial Contributor(s): Leonid Kostrykin, Beatriz Serrano-Solano, Riccardo Massei

Funder(s): Deutsche Forschungsgemeinschaft

Grants(s): NFDI4Bioimage

gtn star logo followed by the word workflows

Inputs

ID Name Description Type
Ground Truth Image Ground Truth Image Input the ground truth image
  • File
Image to segment Image to segment Upload an image or provide a dataset to initiate the image segmentation process.
  • File
Sigma Values Sigma Values Input a series of sigma values as tabular file
  • File

Steps

ID Name Description
3 Split by group toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.6
4 Parse parameter value param_value_from_file
5 Filter 2-D image toolshed.g2.bx.psu.edu/repos/imgteam/2d_simple_filter/ip_filter_standard/1.12.0+galaxy1
6 Perform histogram equalization toolshed.g2.bx.psu.edu/repos/imgteam/2d_histogram_equalization/ip_histogram_equalization/0.18.1+galaxy0
7 Threshold image toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy3
8 Compute image segmentation and object detection performance measures toolshed.g2.bx.psu.edu/repos/imgteam/segmetrics/ip_segmetrics/1.4.0-2
9 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

Outputs

ID Name Description Type
output output n/a
  • File

Version History

1.0 (earliest) Created 2nd Jun 2025 at 10:56 by GTN Bot

Added/updated 4 files


Open master 48c65c1
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
License
Activity

Views: 40   Downloads: 3   Runs: 0

Created: 2nd Jun 2025 at 10:56

help Attributions

None

Total size: 83 KB
Powered by
(v.1.17.0-main)
Copyright © 2008 - 2025 The University of Manchester and HITS gGmbH