CP_pipeline_IDR_training

imaging-tutorial-CP/main-workflow

Author(s)

version Version
3
last_modification Last updated
Nov 4, 2020
license License
None Specified, defaults to CC-BY-4.0
galaxy-tags Tags
CellProfiler
imaging

Features

Tutorial
hands_on Nucleoli segmentation and feature extraction using CellProfiler

Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness purl PURL
https://gxy.io/GTN:W00106
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode question
galaxy-download Download
flowchart TD
  0["Starting modules"];
  1["Download images"];
  2["Segment complete nuclei"];
  0 -->|output_pipeline| 2;
  3["Segmentation mask complete nuclei"];
  2 -->|output_pipeline| 3;
  4["Label nuclei"];
  3 -->|output_pipeline| 4;
  5["Save labelled nuclei"];
  4 -->|output_pipeline| 5;
  6["Detect dark holes in nuclei"];
  5 -->|output_pipeline| 6;
  7["Segment nucleoli that fall inside nuclei"];
  6 -->|output_pipeline| 7;
  8["Segment nucleoli"];
  7 -->|output_pipeline| 8;
  9["Convert the segmented nucleoli into an image"];
  8 -->|output_pipeline| 9;
  10["Combine masks nuclei + nucleoli"];
  9 -->|output_pipeline| 10;
  11["Save combined segmentation masks"];
  10 -->|output_pipeline| 11;
  12["Segment all nuclei"];
  11 -->|output_pipeline| 12;
  13["Segmentation mask nucleoli including cells touching borders"];
  12 -->|output_pipeline| 13;
  14["Extract background"];
  13 -->|output_pipeline| 14;
  15["Measure the image granularity"];
  14 -->|output_pipeline| 15;
  16["Measure the nuclei texture"];
  15 -->|output_pipeline| 16;
  17["Measure the nuclei intensity"];
  16 -->|output_pipeline| 17;
  18["Measure size and shape of nuclei and nucleoli"];
  17 -->|output_pipeline| 18;
  19["Relate nucleoli with their parent nuclei"];
  18 -->|output_pipeline| 19;
  20["Measure the image quality"];
  19 -->|output_pipeline| 20;
  21["Measure the area occupied by nuclei and nucleoli"];
  20 -->|output_pipeline| 21;
  22["Measure the image intensity"];
  21 -->|output_pipeline| 22;
  23["Export measurements"];
  22 -->|output_pipeline| 23;
  24["Run CellProfiler"];
  1 -->|output_tar| 24;
  23 -->|output_pipeline| 24;

Inputs

Input Label

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9 Starting Modules Starting modules
toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41 IDR Download Download images
toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 IdentifyPrimaryObjects Segment complete nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 ConvertObjectsToImage Segmentation mask complete nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9 DisplayDataOnImage Label nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 SaveImages Save labelled nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9 EnhanceOrSuppressFeatures Detect dark holes in nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9 MaskImage Segment nucleoli that fall inside nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 IdentifyPrimaryObjects Segment nucleoli
toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 ConvertObjectsToImage Convert the segmented nucleoli into an image
toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9 GrayToColor Combine masks (nuclei + nucleoli)
toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 SaveImages Save combined segmentation masks
toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 IdentifyPrimaryObjects Segment all nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 ConvertObjectsToImage Segmentation mask nucleoli including cells touching borders
toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0 ImageMath Extract background
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9 MeasureGranularity Measure the image granularity
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9 MeasureTexture Measure the nuclei texture
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9 MeasureObjectIntensity Measure the nuclei intensity
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9 MeasureObjectSizeShape Measure size and shape of nuclei and nucleoli
toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9 RelateObjects Relate nucleoli with their parent nuclei
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9 MeasureImageQuality Measure the image quality
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9 MeasureImageAreaOccupied Measure the area occupied by nuclei and nucleoli
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9 MeasureImageIntensity Measure the image intensity
toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9 ExportToSpreadsheet Export measurements
toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9 CellProfiler Run CellProfiler

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41 View in ToolShed

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on galaxy-upload Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
7 bd719212c 2020-11-04 12:16:00 Update main_workflow.ga
6 e06005125 2020-11-04 11:18:23 add missing annotation field
5 ceef3fe07 2020-11-03 22:54:32 add tag imaging
4 28a7fb28b 2020-11-03 22:46:53 Update main_workflow.ga
3 a3a14fb90 2020-06-24 12:16:10 add annotation and tags to the wf
2 8fdf6cf2d 2020-06-24 11:43:50 format wf
1 82051aef7 2020-06-19 09:24:49 training_init

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows