flowchart TD
0["Starting modules"];
1["Download images"];
2["Segment complete nuclei"];
0 -->|output_pipeline| 2;
3["Segmentation mask complete nuclei"];
2 -->|output_pipeline| 3;
4["Label nuclei"];
3 -->|output_pipeline| 4;
5["Save labelled nuclei"];
4 -->|output_pipeline| 5;
6["Detect dark holes in nuclei"];
5 -->|output_pipeline| 6;
7["Segment nucleoli that fall inside nuclei"];
6 -->|output_pipeline| 7;
8["Segment nucleoli"];
7 -->|output_pipeline| 8;
9["Convert the segmented nucleoli into an image"];
8 -->|output_pipeline| 9;
10["Combine masks nuclei + nucleoli"];
9 -->|output_pipeline| 10;
11["Save combined segmentation masks"];
10 -->|output_pipeline| 11;
12["Segment all nuclei"];
11 -->|output_pipeline| 12;
13["Segmentation mask nucleoli including cells touching borders"];
12 -->|output_pipeline| 13;
14["Extract background"];
13 -->|output_pipeline| 14;
15["Measure the image granularity"];
14 -->|output_pipeline| 15;
16["Measure the nuclei texture"];
15 -->|output_pipeline| 16;
17["Measure the nuclei intensity"];
16 -->|output_pipeline| 17;
18["Measure size and shape of nuclei and nucleoli"];
17 -->|output_pipeline| 18;
19["Relate nucleoli with their parent nuclei"];
18 -->|output_pipeline| 19;
20["Measure the image quality"];
19 -->|output_pipeline| 20;
21["Measure the area occupied by nuclei and nucleoli"];
20 -->|output_pipeline| 21;
22["Measure the image intensity"];
21 -->|output_pipeline| 22;
23["Export measurements"];
22 -->|output_pipeline| 23;
24["Run CellProfiler"];
1 -->|output_tar| 24;
23 -->|output_pipeline| 24;
To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.
Importing into Galaxy
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
Click on galaxy-uploadImport at the top-right of the screen
Provide your workflow
Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
Click the Import workflow button
Below is a short video demonstrating how to import a workflow from GitHub using this procedure:
Download Workflow RO-Crate
View on WorkflowHub