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

SEEK ID: https://workflowhub.eu/workflows/41?version=2

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