diff --git a/README.md b/README.md index 6fedb93..b6b45a8 100644 --- a/README.md +++ b/README.md @@ -10,26 +10,37 @@ Interactive in silico fate mapping from tracking data. -This napari plugin allows the estimation o cell fates from incomplete tracking data by building a radial regression model per time point. The user can interrogate different starting (ending) positions using a `Points` layer; the application will advent the probed coordinates forward (backward) in time, showing the estimated fate. +This napari plugin estimates the cell fates from tracking data by building a radial regression model per time point. The user can select an area of interest using a `Points` layer; the algorithm will advent the probed coordinates forward (or backward) in time, showing the estimated fate. Video example below: - - -TODO: add to pypi +https://user-images.githubusercontent.com/21022743/216478216-89c1c35f-2ce4-44e8-adb8-9aeea75b5833.mp4 ## Installation +TODO: add to pypi + You can install `in-silico-fate-mapping` via [pip]: pip install in-silico-fate-mapping -To install latest development version : +To install the latest development version : pip install git+https://github.com/royerlab/in-silico-fate-mapping.git + +## IO file format + +This plugin does not depend on a specific file format, the only requirement is using a `Track` layer from napari. + +Despite this, we ship a reader and writer interface. It supports `.csv` files with the following reader `TrackID, t, (z), y, x`, `z` is optional. +Such that each tracklet has a unique `TrackID` and it's composed of a sequence o time and spatial coordinates. + +This is extremely similar to how napari store tracks, more information can be found [here](https://napari.org/stable/howtos/layers/tracks.html). + +Divisions are not supported at the moment. + ## Citing If used please cite: