Workflow Type: Galaxy
Open
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.
Steps
ID | Name | Description |
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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 |
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_anonymous_output_1 | _anonymous_output_1 | n/a |
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_anonymous_output_2 | _anonymous_output_2 | n/a |
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_anonymous_output_3 | _anonymous_output_3 | n/a |
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_anonymous_output_4 | _anonymous_output_4 | n/a |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
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_anonymous_output_6 | _anonymous_output_6 | n/a |
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_anonymous_output_7 | _anonymous_output_7 | n/a |
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_anonymous_output_8 | _anonymous_output_8 | n/a |
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_anonymous_output_9 | _anonymous_output_9 | n/a |
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_anonymous_output_10 | _anonymous_output_10 | n/a |
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_anonymous_output_11 | _anonymous_output_11 | n/a |
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_anonymous_output_12 | _anonymous_output_12 | n/a |
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_anonymous_output_13 | _anonymous_output_13 | n/a |
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_anonymous_output_14 | _anonymous_output_14 | n/a |
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_anonymous_output_15 | _anonymous_output_15 | n/a |
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_anonymous_output_16 | _anonymous_output_16 | n/a |
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_anonymous_output_17 | _anonymous_output_17 | n/a |
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_anonymous_output_18 | _anonymous_output_18 | n/a |
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_anonymous_output_19 | _anonymous_output_19 | n/a |
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_anonymous_output_20 | _anonymous_output_20 | n/a |
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_anonymous_output_21 | _anonymous_output_21 | n/a |
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_anonymous_output_22 | _anonymous_output_22 | n/a |
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_anonymous_output_23 | _anonymous_output_23 | 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: 7465 Downloads: 595 Runs: 0
Created: 24th Jun 2020 at 22:00
Last updated: 19th Jun 2023 at 13:40
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