BERA Tools

BERA Tools is successor of Forest Line Mapper. It is a toolset for enhanced delineation and attribution of linear disturbances in forests.

Quick Start

Here are the ways to install BERA Tools:

• Windows installer
• Install with Anaconda.

Windows Installer

Windows installer is provided with releases. Check the latest release. Signing is currently off by default; unsigned assets are named beratools-installer-x.y.z-unsigned.exe and identified as unsigned in the release notes. Windows may display an unknown-publisher or SmartScreen warning. Maintainers can enable SignPath per run according to the BERA Tools Code signing policy.

Install with Anaconda

Install with Anaconda works on Windows, macOS, and Linux.

• Install Miniconda. Download Miniconda from Miniconda and install on your machine.

• Download and save the file environment.yml.

• Launch Anaconda Prompt and Change directory to where environment.yml is saved.

• Run the command to install BERA Tools.

  $ conda env create -n bera -f environment.yml

  After the installation is done, a new environment named bera is created and BERA Tools is installed within it.

• Activate the bera environment and launch BERA Tools main GUI:

  $ conda activate bera
  $ beratools gui

• Download latest example data to try with BERA Tools.

For more information about installation, check the BERA Tools Installation.

Troubleshooting: CondaEnvException: Pip failed

environment.yml installs rpy2 with pip at the end of conda env create. If that step fails (e.g. Pip subprocess error), create the environment without pip first, then install rpy2 yourself:

1. Open environment.yml and comment out the pip section:

   #  - pip:
   #      - rpy2

2. Create and activate the environment:

   $ conda env create -n bera -f environment.yml
   $ conda activate bera

3. Set the R paths (Windows Anaconda Prompt):

   set "R_HOME=%CONDA_PREFIX%\Lib\R"
   set "PATH=%R_HOME%\bin\x64;%PATH%"

4. Install rpy2 with pip:

   $ python -m pip install rpy2

If pip still fails, check that the environment's Python starts with python -c "print('ok')". A Python that does not start (e.g. "The file or directory is corrupted and unreadable") is the real cause. Rebuild the environment with a different Python version.

PC2Products (LiDAR) Tools

The PC2Products (Point Cloud to Products) category turns LiDAR point clouds (.las / .laz) into rasters such as a DTM, DSM, CHM and hummock/hollow maps. The tools run R and lidR through rpy2; environment.yml and pixi.toml include R, and the tools install the R packages they need the first time they run (see R for the PC2Products tools).

Tool	bt subcommand
LiDAR data info	las_info
Raster Cell size from LiDAR data	cellsize
Ground Classify Using CSF	gnd_csf
Generate DTM from LiDAR Data	dtm
Normalize LiDAR Data	normalize
Generate CHM or DSM from LiDAR Data	chm_dsm
Detect Hummock and Hollow from LiDAR Data	hh
Surface Water Mapping	surface_water
Depth-to-Water from Surface Water	dtw
Seismic Line Disturbance Analysis	line_analysis

$ beratools dtm --in_las_folder tests/data/LiDAR --out_folder tests/data/LiDAR/Raster_Output --style tin

Sample tiles are in tests/data/LiDAR/, and examples/ has two scripts that run the LiDAR tools in sequence (see examples/README.md).

Pipelines

The Pipeline tab, next to Tool history in the GUI, chains tools into steps that run one after another. Drag tools in from the tool tree, set each step's parameters in the tool form, and link a step's inputs to an earlier step's output. Each input links to the latest earlier step that makes what it needs, for example a CHM from Generate CHM or DSM from LiDAR Data into Centerline, and the links are reset whenever a step is added, moved or removed. Pipelines save as .json files and also run without the GUI:

$ python -m beratools.core.pipeline my_pipeline.json --processes 4

See Building a pipeline.

BERA Tools Guide

Check the online BERA Tools Guide for user, developer and technical guides.

Sponsors

Free code signing on Windows provided by SignPath.io, certificate by SignPath Foundation.

Credits

This tool is part of the Boreal Ecosystem Recovery & Assessment (BERA). It is actively developed by the Applied Geospatial Research Group. © 2026 Applied Geospatial Research Group. All rights reserved.