ArcGIS Toolbox for Landscape Limnology
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This is an ArcGIS toolbox for landscape limnology created from a collection of Python script tools. It was used to create the LAGOS-NE database and is currently being updated in 2017 and 2018 for the creation of the LAGOS-US database.

This toolbox was created with ArcGIS 10.1. It is being maintained in ArcGIS 10.3. It may work for other versions of ArcGIS.

Releases & Citation

Release v1.0 corresponds to the methods documented in the following manuscript:

Soranno, P. A., Bissell, E. G., Cheruvelil, K. S., Christel, S. T., Collins, S. M., Fergus, C. E., ... & Scott, C. E. (2015). Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse. GigaScience, 4(1), 28.


  • Spatial Analyst extension (some tools)
  • RivEX software (proprietary) to create the input (rivers with Strahler order assignment) to the Lake Order Tool.
  • While some steps in our workflow at Michigan State University are conducted in a supercomputing environment (ie Taudem pitremove & d8flowdir were ported to RHEL to get the data processed faster), you can do these steps on a workstation easily enough with ESRI tools or with the Taudem tool suite.


  • Open the ArcToolbox Pane

  • Right click to access the Add Toolbox command

  • Navigate to LAGOS_GIS_Toolbox.tbx

  • (Optional) Right click on ArcToolbox root, then click "Save Settings > To Default" to save this toolbox to your default tools


Lake Analysis

  • Lake Connectivity Classification
  • Lake Order Classification
  • Lake-Wetland Connections
  • Upstream Lakes

Summarize Data by Zones

  • Lakes in Zones
  • Line Density
  • Point Density
  • Polygons in Zones
  • Streams in Zones
  • Subset Overlapping Zones
  • Wetlands in Zones
  • Zonal Attribution of Raster Data


  • Add Unique Fields
  • Drop Fields and Calc Geometry
  • Export to CSV
  • Merge Many Feature Classes
  • Merge Many Shapefiles
  • Merge NHD Features
  • Merge NHD Features without Deduplication
  • Mosaic to Subregion
  • Prefix Field Names

Watershed Delineation

  1. State and Mosaic Data for Subregion
  2. Burn Flowlines into DEM
  3. Clip DEM to HU8 Boundaries
  4. (Step 4 (Fill Pits) is not in toolbox)
  5. Create HU8 Walls
  6. (Step 6 (Flow Direction) is not in toolbox)
  7. Convert TauDEM Flow Direction Raster to ArcGIS Format
  8. Create Pour Points
  9. Create Lake Watersheds

Wetland Analysis

  1. Preprocess NWI
  2. Wetland Order

The toolbox is not formally supported. You can direct questions to the current maintainer, Nicole Smith (, or the project PI, Patricia Soranno (