3Dtrees: From LiDAR point clouds to individual trees

Run Workflow in Galaxy

• Galaxy France
• Galaxy Main
• Galaxy Australia
• Galaxy Europe
• Galaxy Canada
• Import to another server (≥23.0+ only!)

flowchart TD
  0["ℹ️ Input Dataset\nPoint cloud LAS/LAZ"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Standardization"];
  0 -->|output| 1;
  83d15133-429b-4530-92a6-b4375659c96a["Output\nstandardized"];
  1 --> 83d15133-429b-4530-92a6-b4375659c96a;
  style 83d15133-429b-4530-92a6-b4375659c96a stroke:#2c3143,stroke-width:4px;
  dd737f4c-d36f-4e8a-924b-9c4a93dfe3fb["Output\nmetadata"];
  1 --> dd737f4c-d36f-4e8a-924b-9c4a93dfe3fb;
  style dd737f4c-d36f-4e8a-924b-9c4a93dfe3fb stroke:#2c3143,stroke-width:4px;
  ee84fd37-a142-4313-ade6-170efc14298c["Output\nconvex_hull"];
  1 --> ee84fd37-a142-4313-ade6-170efc14298c;
  style ee84fd37-a142-4313-ade6-170efc14298c stroke:#2c3143,stroke-width:4px;
  2["SmartTile: tile and subsample"];
  1 -->|pc_standardized| 2;
  23a23ea1-11e8-4fd8-a146-a3c346aa3c87["Output\ntiling_preview"];
  2 --> 23a23ea1-11e8-4fd8-a146-a3c346aa3c87;
  style 23a23ea1-11e8-4fd8-a146-a3c346aa3c87 stroke:#2c3143,stroke-width:4px;
  3["Overviews"];
  1 -->|pc_standardized| 3;
  106bb3bb-3c02-4278-b940-8bedf2e62625["Output\ntop_views"];
  3 --> 106bb3bb-3c02-4278-b940-8bedf2e62625;
  style 106bb3bb-3c02-4278-b940-8bedf2e62625 stroke:#2c3143,stroke-width:4px;
  e1c3b905-0f92-4682-b4dc-62d0b0924492["Output\nsection_views"];
  3 --> e1c3b905-0f92-4682-b4dc-62d0b0924492;
  style e1c3b905-0f92-4682-b4dc-62d0b0924492 stroke:#2c3143,stroke-width:4px;
  4["SegmentAnyTree"];
  2 -->|output_tiles_1| 4;
  1fc91bea-39cf-4988-8f26-a57b7e9658ce["Output\nsegmented"];
  4 --> 1fc91bea-39cf-4988-8f26-a57b7e9658ce;
  style 1fc91bea-39cf-4988-8f26-a57b7e9658ce stroke:#2c3143,stroke-width:4px;
  5["SmartTile: filter / merge and remap"];
  4 -->|output| 5;
  2 -->|tile_bounds_json| 5;
  1 -->|pc_standardized| 5;
  485e2984-0a2c-47e5-8275-98a533701d29["Output\noriginals_with_predictions"];
  5 --> 485e2984-0a2c-47e5-8275-98a533701d29;
  style 485e2984-0a2c-47e5-8275-98a533701d29 stroke:#2c3143,stroke-width:4px;
  6["Potree"];
  5 -->|output_originals_with_dims| 6;
  103bc632-ed3a-4e66-996b-5df8614063a7["Output\npotree_viewer"];
  6 --> 103bc632-ed3a-4e66-996b-5df8614063a7;
  style 103bc632-ed3a-4e66-996b-5df8614063a7 stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

Tools

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/climate/tutorials/3dtrees/workflows/main_workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows