Quantitative Morphogenesis Laboratory

University of Toronto

PyJAMAS links


PyJAMAS plugins

Batch compute weight maps - Ray Hawkins - create neural network weight maps for entire datasets.

Export text annotations - Rodrigo Fernandez-Gonzalez - exports PyJAMAS annotations to a text file.

FCS - Rodrigo Fernandez-Gonzalez - fluorescence correlation spectroscopy analysis.

Polyline ID tools - Ray Hawkins - tools for interactively editing polyline IDs.

Recoil velocity - Rodrigo Fernandez-Gonzalez - analyze laser ablation experiments (includes recoil velocity analysis and Kelvin-Voigt modelling)

Recoil area - Rodrigo Fernandez-Gonzalez - analyze circular laser ablation experiments (useful to quantify the mechanics of small tissue patches)

Slipper (Slice Flipper) - Ray Hawkins - automatically corrects flipped slices between video channels.

Time difference - Rodrigo Fernandez-Gonzalez - calculates the difference in pixel values across slices (i.e. a gradient along the third dimension of an image stack).

Tricellular Junction Automated Detection - Ray Hawkins - pipeline for detecting tricellular junctions and refining tricellular junction annotations.

Wire connect - Rodrigo Fernandez-Gonzalez - connects two points using Dijkstra's minimal cost path algorithm. Can be applied iteratively over multiple image slices.