Matt Smith

POSTDOCTORAL TRAINING FELLOW

I am a senior postdoc in Guillaume Salbreux's Lab. I am developing tools to perform image analysis on 3D cell colonies. Some of the projects I am working on:

Creating interactive software using active contours that deform to capture the shape of 3D cells.

Developing NN models to leverage AI for detecting cells.

Making tools for data visualization.

Images

Different stages of a mesh: initialization, deformed to the original image, deformed to the distance transform, comparing the nucleus, manually initialized mesh and an auto-detected membrane mesh.

Different stages of a mesh: initialization, deformed to the original image, deformed to the distance transform, comparing the nucleus, manually initialized mesh and an auto-detected membrane mesh.  

Time lapse of an organoid that has been segmented over time. The top row shows the complete meshes, and the bottom row show the trajectories of a single lineage, from one cell two four cells after two rounds of mitosis.

Time lapse of an organoid that has been segmented over time. The top row shows the complete meshes, and the bottom row show the trajectories of a single lineage, from one cell two four cells after two rounds of mitosis.

Using our FiJi plugin DM3D to draw spheres for initializing a mesh

Using our FiJi plugin DM3D to draw spheres for initializing a mesh.

A cell with the membrane segmented, and the corresponding average curvature.

A cell with the membrane segmented, and the corresponding average curvature.