Welcome to HCAT’s documentation!

HCAT - Hair Cell Analysis Toolbox

Hcat is a suite of machine learning enabled algorithms for performing common image analyses in the hearing field.

Quickstart Guide


  1. Install Anaconda

  2. Perform the installation by copying and pasting the following comands into your Anaconda Prompt (Windows) or Terminal (Max/Linux)

  3. Create a new anaconda environment: conda create -yn hcat python=3.9

  4. Activate the anaconda environment: conda activate hcat


You will need to avtivate your conda environment every time you restart your prompt!

  1. Install pytorch for CPU ONLY: conda install pytorch torchvision torchaudio cpuonly -c pytorch

  2. Install hcat and dependencies: pip install hcat --upgrade

  3. Run hcat: hcat


Follow the detailed installation guide for instructions on how to enable GPU acceleration


Detection Gui:

  • Run in terminal: hcat

CLI Hair Cell Detection Analysis:

  • Run in terminal: hcat detect "path/to/file.tif"

Analysis Entrypoints:

API Guide: