CP_pipeline_IDR_training
3.0

Workflow Type: Galaxy

Nucleoli segmentation and feature extraction using CellProfiler

Associated Tutorial

This workflows is part of the tutorial Nucleoli segmentation and feature extraction using CellProfiler, available in the GTN

Thanks to...

Tutorial Author(s): Beatriz Serrano-Solano, Jean-Karim Hériché

Tutorial Contributor(s): Helena Rasche, Saskia Hiltemann, Björn Grüning, Beatriz Serrano-Solano, Anne Fouilloux

gtn star logo followed by the word workflows

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
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_anonymous_output_10 #main/_anonymous_output_10 n/a
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_anonymous_output_11 #main/_anonymous_output_11 n/a
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_anonymous_output_12 #main/_anonymous_output_12 n/a
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_anonymous_output_13 #main/_anonymous_output_13 n/a
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_anonymous_output_14 #main/_anonymous_output_14 n/a
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_anonymous_output_15 #main/_anonymous_output_15 n/a
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_anonymous_output_16 #main/_anonymous_output_16 n/a
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_anonymous_output_17 #main/_anonymous_output_17 n/a
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_anonymous_output_18 #main/_anonymous_output_18 n/a
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_anonymous_output_19 #main/_anonymous_output_19 n/a
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_anonymous_output_2 #main/_anonymous_output_2 n/a
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_anonymous_output_20 #main/_anonymous_output_20 n/a
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_anonymous_output_21 #main/_anonymous_output_21 n/a
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_anonymous_output_22 #main/_anonymous_output_22 n/a
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_anonymous_output_23 #main/_anonymous_output_23 n/a
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_anonymous_output_24 #main/_anonymous_output_24 n/a
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_anonymous_output_25 #main/_anonymous_output_25 n/a
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_anonymous_output_26 #main/_anonymous_output_26 n/a
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_anonymous_output_3 #main/_anonymous_output_3 n/a
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_anonymous_output_4 #main/_anonymous_output_4 n/a
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_anonymous_output_5 #main/_anonymous_output_5 n/a
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_anonymous_output_6 #main/_anonymous_output_6 n/a
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_anonymous_output_7 #main/_anonymous_output_7 n/a
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_anonymous_output_8 #main/_anonymous_output_8 n/a
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_anonymous_output_9 #main/_anonymous_output_9 n/a
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Version History

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

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