Skeletal Muscle Imaging Toolbox

Distributing tools and pipelines for scientific skeletal muscle imaging in ImageJ and Fiji.

Table of Contents

• Introduction
• Pipelines
• Contributing
• License

Introduction

This resource serves to collect, distribute, and document pipelines and tools relating to skeletal muscle imaging, particularly those that operate within FIJI and ImageJ.

The main goal is to provide all the plugins in one repository, such that users can easily find and use them. If this proves to be helpful, it can be turned into an ImageJ Update Site.

If you DO use any of the tools in this toolbox, remember to cite the original author using the table below!

Usage

To install the whole toolbox, simply download the latest release Skeletal_Muscle_Toolbox.jar file into your Fiji.app/jars/ directory. After Fiji is restarted, all pipelines should be available under a single submenu in the Plugins dropdown (and discoverable via the Command Finder).

Alternatively, follow the links in the pipelines below to get retrieve just one pipeline.

Pipelines

Pipeline Name and Publication	Description	Source-code	Citation + DOI	License	Distributed with Skeletal Muscle Toolbox
TrueFAD_Histo	Modern fully-automated end-to-end deep-learning pipeline for histology and myotube measurement	GitHub	Brun et al., 2024	GPL3	Yes
MuscleJ2	Modern fully-automated end-to-end pipeline supporting a variety of outputs	GitHub	Danckaert et al., 2023	CC0, as per journal
LabelsToROIs	Converter from Label-Images to ROIs + ROI erosion.	GitHub	Waisman et al., 2021	GPL3	Yes
MyoSight	End-to-end semi-automated pipeline	GitHub	Babcock et al., 2020	CC0 as per journal	Yes
Myosoft	Fiber-Typing of using Machine-Learning Algorithm	GitHub	Encarnacion-Rivera et al., 2020	GPL3 (via source code)	Yes (Version 15)
MyoSAT	Muscle imaging pipeline for H&E stained samples	GitHub	Stevens et al., 2020	CC-BY-4.0 as per journal	Yes (Version 3.5)
Open-CSAM	Semi-automatic ImageJ processing macro	PDF Download	Desgeorges et al., 2019	CC-BY-4.0, as per journal	Yes
Fernandez	Fiber Morphometry and Fiber-Type of Human Skeletal Muscle.	IJM	Reyes-Fernandez et al., 2019	CC0, as per journal	Yes
Bonilla	A heavily modified version of MuscleJ for human skeletal muscle.	IJM 1 & IJM 2	Bonilla et al., 2018	GPL3 (via source code)	Yes
MuscleJ	Open-source automatic pipeline (Deprecated for MuscleJ2)	GitHub	Mayeuf-Louchart et al., 2018	GPL3

Pipeline Feature Comparison

(Under construction)

Feature	FT	NUC	MEAS	VAS	SAT	FLUOR	H&E	ML/DL
TrueFAD_Histo	✅	☐	✅	☐	☐	✅	☐	✅
MuscleJ2	✅	✅	✅	✅	✅	✅	☐	☐
LabelsToROIs	☐	☐	☐	☐	☐	☐	☐	☐
MyoSight	✅	✅	✅	☐	☐	✅	☐	☐
Myosoft	✅	☐	☐	☐	☐	☐	☐	✅
MyoSAT	☐	☐	☐	☐	☐	☐	✅	☐
Open-CSAM	☐	☐	✅	☐	☐	☐	☐	☐
Fernandez	☐	☐	☐	☐	☐	☐	☐	☐
MuscleJ	☐	☐	☐	☐	☐	☐	☐	☐
Bonilla	☐	☐	☐	☐	☐	☐	☐	☐

*If the plugin has no name, the first authors surname was used as an identifier.

Abbreviations:

• FT : Provides Fiber-Typing
• NUC : Provides Fiber Nucleation (Central/Peripheral)
• MEAS : Morphological measures (CSA/Feret)
• VAS : Can annotate capillaries/vasculature
• SAT : Can annotate satellite cells
• FLUOR : Compatible with fluorescence imaging
• H&E : Compatible with H&E staining
• ML/DL : Machine/Deep Learning

Criteria

Software referenced here must:

1. Provide functionality for skeletal muscle imaging
2. Be in the form of a macro, script, or ImageJ/FIJI plugin
3. Operate within the FIJI/ImageJ environment
4. Be publically accessible.

Software distributed here must

1. Be licensed appropriately for redistribution
2. Be open-source

Contributing

Contributions are welcome! If you have a pipeline or muscle-imaging tool to add, please follow these steps:

1. Fork the repository.
2. Create a new branch (git checkout -b new-branch).
3. Make and commit your changes (git commit -m 'Add new pipeline').
4. Push to the branch (git push origin new-branch).
5. Open a Pull Request to the main branch

License

This repository is licensed under the MIT License. Please ensure that you comply with the licenses of the individual pipelines included in this repository.