GUI Usage

SarcAsM’s GUI application uses Napari image browser as image viewer. Check out this page for a primer on Napari’s GUI.

Starting the App

There are two main ways to start the SarcAsM GUI:

1. Standalone Applications (Recommended for ease of use):

  • Pre-built applications for Windows (.exe) and macOS (.app) are available for download directly from the GitHub Releases page.

  • This method does not require a separate Python installation.

  • Note:

    • These standalone applications are early versions and may take a significant amount of time to start up initially.

    • They are built using Python 3.11.

    • The Windows version currently only utilizes the CPU and does not support CUDA GPU acceleration. For high-performance needs, consider using the Python API.

2. From your Python Environment (Recommended for developers or API users):

  • If you have installed SarcAsM into a Python environment (e.g., via pip or conda):

  • First, remember to activate your installation environment:

    conda activate sarcasm-env # Or your specific environment name

  • Then, to start the app, run this command:

    python -m sarcasm_app

Using the App

Screenshot of the SarcAsM application GUI

The SarcAsM GUI integrates controls (left panel) with a Napari image viewer (right panel). Follow the steps in the control panel sections for analysis.

Initial Steps:

  1. Load File: Use Search in File Selection to load a grayscale TIFF file.

  2. Set Metadata: In Metadata, check the Pixel size [µm]. If the field is red or incorrect, enter the correct value and press Store Metadata.

Analysis Sections:

Proceed through the collapsible sections in the control panel:

  • Parameter import/export: Load/save analysis settings or reset to defaults.

  • Structure Analysis: Analyze sarcomere structure.

  • LOI Finder: Find and/or draw Lines of Interest (requires structure results).

  • Motion Analysis: Analyze sarcomere motion in LOIs.

  • Batch Processing: Process multiple files automatically.

Using Parameters:

  • Tooltips: Hover over parameter names/fields for descriptions.

  • If needed, optimize settings within each section before running the corresponding analysis step (e.g., clicking Detect sarcomeres).