Software Tools I’ve Developed Link to heading

I’ve developed a number of software tools for imaging, deep-learning, and biological modelling. The ones here are designed to help practitioners with image analysis. Tools without links are still in development.

General Link to heading

[Conda/Mamba] iconda: A lightweight GUI for conda environment handling and creation of common scientific deep-learning environments.

Imaging Link to heading

[Fiji/ImageJ] FiberSight A full skeletal muscle cross-section imaging analysis suite. Provides several functionalities.

[Fiji/ImageJ] Fiji Border Exclusion: Plugin for Fiji/ImageJ. Solves the problem of manually removing ROIs and Labels from a specified area.

[Fiji/ImageJ] JInspect Allows you to leverage the ImageJ/Fiji script editor to inspect the methods and attributes of objects.

[Fiji/ImageJ] Skeletal Muscle Toolbox: An aggregation of every available open-source skeletal muscle imaging tool.

[Napari] Napari Labeller A tool for quickly creating Ground Truth image instance labels for training ML models.

Biological Modelling Link to heading

[RShiny] Alon Oscillators An RShiny App showing solvers for biological oscillations

[RShiny] Bayesian Clonal Diversity A Shiny App allowing you to approximate the species diversity of a subsample of a population.