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.

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Quickstart Guide

Installation

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

Warning

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

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

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

7. Run hcat: hcat

Note

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

Analysis

Detection Gui:

• Run in terminal: hcat

CLI Hair Cell Detection Analysis:

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

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Instructions

• Detailed Installation
• Use the Detection Gui
• Use the Comand Line Interface
  • Detect
  • Common Issues

Analysis Entrypoints:

• detect

API Guide:

• hcat.lib
• hcat.backends