Nucleoli segmentation using CellProfiler (EOSC-Life D6)
Version 2

Workflow Type: Galaxy
Stable

This workflow has been created as part of Demonstrator 6 of the project EOSC-Life (within WP3) and is focused on reusing publicly available RNAi screens to gain insights into the nucleolus biology. The workflow downloads images from the Image Data Resource (IDR), performs object segmentation (of nuclei and nucleoli) and feature extraction of the images and objects identified.

Tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/tutorial-CP/tutorial.html

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 _anonymous_output_1 n/a
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_anonymous_output_3 _anonymous_output_3 n/a
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_anonymous_output_24 _anonymous_output_24 n/a
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_anonymous_output_25 _anonymous_output_25 n/a
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_anonymous_output_26 _anonymous_output_26 n/a
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Version History

Version 2 (latest) Created 3rd Nov 2020 at 22:12 by Beatriz Serrano-Solano

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Views: 5425   Downloads: 347

Created: 24th Jun 2020 at 22:00

Last updated: 19th Jun 2023 at 13:40

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