PyJAMAS links
documentation (contains installation instructions)
app (MacOS-Silicon, MacOS-Intel, Windows 11)
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.
Photobleaching correction - Negar Balaghi - correct open image for photobleaching.
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).
Track polylines - Ray Hawkins - uses fiducial id's to track containing polylines.
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.