Automated Muscle Morphometry

Machine learning based software for whole slide morphometric analysis of human biopsied muscle on H&E.

Installation

Clone the Hifuku GitHub repository:

git clone https://github.com/onnonuro/mmmetry.git

Tutorial with Google Colab

Google Colab is the easiest way to try this software with GPU support, especially for clinicians and pathologists who are unfamiliar with programming or do not have a local Python environment.

To get started:

1. Download tutoial.ipynb: Download tutoial.ipynb.

2. Upload tutoial.ipynb to your Google Drive: Upload the file to your Google Drive.

3. Open tutoial.ipynb with Google Colab: Sign in Google Colab and open tutoial.ipynb with it.

4. Run mmmetry: Follow the instructions in the Jupyter Notebook tutorial.

   *You need a google account and sign in to Google colab.

Dependencies

This software was tested in the following Google Clolab environment on June 4, 2024.

Python (3.10.12), torch (2.1.0+cu118), torchvision (0.16.0+cu118), torchmetrics (1.2.0), pytorch-lightning (2.1.2), segmentation-models-pytorch (0.3.3), timm (0.9.2), opencv-python (4.8.0.76), albumentations (1.3.1)