CP_pipeline_IDR_training
Visit source
Download RO-Crate
Workflow Type: Galaxy
Open
Frozen
Nucleoli segmentation and feature extraction using CellProfiler
Associated Tutorial
This workflows is part of the tutorial CP_pipeline_IDR_training, available in the GTN
Thanks to...
Tutorial Author(s): Beatriz Serrano-Solano, Jean-Karim Hériché
Steps
| ID | Name | Description |
|---|---|---|
| 0 | Starting modules | Detail the metadata associated to the images that will be processed toolshed.g2.bx.psu.edu/repos/bgruening/cp_common/cp_common/3.1.9 |
| 1 | Download images | toolshed.g2.bx.psu.edu/repos/iuc/idr_download_by_ids/idr_download_by_ids/0.41 |
| 2 | Segment complete nuclei | Incomplete nuclei that are touching the borders of the image are ignored and therefore, not segmented. It doesn't include the nuclei outside the diameter range either. toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 3 | Segmentation mask complete nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 4 | Label nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_display_data_on_image/cp_display_data_on_image/3.1.9 |
| 5 | Save labelled nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 |
| 6 | Detect dark holes in nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_enhance_or_suppress_features/cp_enhance_or_suppress_features/3.1.9 |
| 7 | Segment nucleoli that fall inside nuclei | The dark holes enhanced in the previous step are segmented only if they are inside a nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_mask_image/cp_mask_image/3.1.9 |
| 8 | Segment nucleoli | The segmentation only affects those inside the nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 9 | Convert the segmented nucleoli into an image | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 10 | Combine masks (nuclei + nucleoli) | toolshed.g2.bx.psu.edu/repos/bgruening/cp_gray_to_color/cp_gray_to_color/3.1.9 |
| 11 | Save combined segmentation masks | toolshed.g2.bx.psu.edu/repos/bgruening/cp_save_images/cp_save_images/3.1.9 |
| 12 | Segment all nuclei | Incomplete nuclei that are touching the borders of the image are segmented, also the nuclei outside the diameter range. toolshed.g2.bx.psu.edu/repos/bgruening/cp_identify_primary_objects/cp_identify_primary_objects/3.1.9 |
| 13 | Segmentation mask nucleoli including cells touching borders | toolshed.g2.bx.psu.edu/repos/bgruening/cp_convert_objects_to_image/cp_convert_objects_to_image/3.1.9 |
| 14 | Extract background | toolshed.g2.bx.psu.edu/repos/bgruening/cp_image_math/cp_image_math/0.1.0 |
| 15 | Measure the image granularity | This step measures the granularity of the original image toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_granularity/cp_measure_granularity/3.1.9 |
| 16 | Measure the nuclei texture | This step measures the texture of the original image and nuclei in it toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_texture/cp_measure_texture/3.1.9 |
| 17 | Measure the nuclei intensity | This step measures the intensity of the original image and the nuclei toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_intensity/cp_measure_object_intensity/3.1.9 |
| 18 | Measure size and shape of nuclei and nucleoli | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_object_size_shape/cp_measure_object_size_shape/3.1.9 |
| 19 | Relate nucleoli with their parent nuclei | toolshed.g2.bx.psu.edu/repos/bgruening/cp_relate_objects/cp_relate_objects/3.1.9 |
| 20 | Measure the image quality | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_quality/cp_measure_image_quality/3.1.9 |
| 21 | Measure the area occupied by nuclei and nucleoli | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_area_occupied/cp_measure_image_area_occupied/3.1.9 |
| 22 | Measure the image intensity | toolshed.g2.bx.psu.edu/repos/bgruening/cp_measure_image_intensity/cp_measure_image_intensity/3.1.9 |
| 23 | Export measurements | toolshed.g2.bx.psu.edu/repos/bgruening/cp_export_to_spreadsheet/cp_export_to_spreadsheet/3.1.9 |
| 24 | Run CellProfiler | toolshed.g2.bx.psu.edu/repos/bgruening/cp_cellprofiler/cp_cellprofiler/3.1.9 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_10 | #main/_anonymous_output_10 | n/a |
|
| _anonymous_output_11 | #main/_anonymous_output_11 | n/a |
|
| _anonymous_output_12 | #main/_anonymous_output_12 | n/a |
|
| _anonymous_output_13 | #main/_anonymous_output_13 | n/a |
|
| _anonymous_output_14 | #main/_anonymous_output_14 | n/a |
|
| _anonymous_output_15 | #main/_anonymous_output_15 | n/a |
|
| _anonymous_output_16 | #main/_anonymous_output_16 | n/a |
|
| _anonymous_output_17 | #main/_anonymous_output_17 | n/a |
|
| _anonymous_output_18 | #main/_anonymous_output_18 | n/a |
|
| _anonymous_output_19 | #main/_anonymous_output_19 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_20 | #main/_anonymous_output_20 | n/a |
|
| _anonymous_output_21 | #main/_anonymous_output_21 | n/a |
|
| _anonymous_output_22 | #main/_anonymous_output_22 | n/a |
|
| _anonymous_output_23 | #main/_anonymous_output_23 | n/a |
|
| _anonymous_output_24 | #main/_anonymous_output_24 | n/a |
|
| _anonymous_output_25 | #main/_anonymous_output_25 | n/a |
|
| _anonymous_output_26 | #main/_anonymous_output_26 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| _anonymous_output_8 | #main/_anonymous_output_8 | n/a |
|
| _anonymous_output_9 | #main/_anonymous_output_9 | n/a |
|
Version History
3.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master88cf200
7.0 (earliest) Created 25th Jun 2024 at 11:16 by Helena Rasche
Added/updated 4 files
Frozen
7.04c11662
Creators and Submitter
Discussion Channel
Tool
Activity
Views: 615 Downloads: 181
Created: 25th Jun 2024 at 11:16
Last updated: 25th Jun 2024 at 11:16
Tags AttributionsNone
Related items
https://orcid.org/0000-0001-9760-8992
Advanced Spaces list for this Workflow with search and filtering
No description specified
Teams: Testing, Finn's test team, PNDB, LifeMonitorDev, iPC: individualizedPaediatricCure, test, Test Team, Australian BioCommons Dev, opscientia, V-pipe, UX study leave, DALiuGE workflows, Team1, UX study, My Fancy Team, Team UX Study11, My team, ux study team, UX study koehorst, Team Koehorst, UX Study (satra), Steve's UX Study Test Team, TestSaandra, KJ-workflow-test, NewTeam, team, UXStudy, A Team, UX study K, UXStudy99, Study team, Another new team, UX study2, Team 20220225, my new team, UX Study AU, Testing_proteomics, A test space (KKH), Pleiade, QSM4SENIOR, IGG-Bioinfo, Defragmentation training school, FWCC-D@HZDR, Submission Tutorial, Testing team, Galaxy Training Network, Exploring SEEK SOP functionality, MyTest, Tsinghua University BCI group, Test Team Number Nine, Eli's test team, EMBL Bioimage analysis service, Hu's Test
Web page: Not specified
Advanced Teams list for this Workflow with search and filtering
No description specified
Space: General
Public web page: https://galaxy.training
