diff --git a/README.md b/README.md new file mode 100644 index 0000000..7aea78f --- /dev/null +++ b/README.md @@ -0,0 +1,16 @@ +# DOG +A Jython script for [Fiji/ImageJ](https://github.com/fiji) to perform [Difference of Gaussians](http://en.wikipedia.org/wiki/Difference_of_Gaussians) on fluorescent stack and plot the result. + +This script will open a single channel fluorescent stack, perform the Difference of Gaussians and then plot all found points with the orthoslice view + +## Parameters available : +- cellDiameter : select the cell/nucleus diameter (in unit of the Image Stack) +- minPeak : min intensity for a peak to be considered +- plotType : plot Points, Icospheres or limit to the first 3495 points due to some slowdown with Icospheres +- cellIcosophere : size of the point/icosphere use to visualize each detected point. + +## TODO: +- Apply 3D Watershed segmentation using the detected points has a seed (see [3D Watershed plugin](http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start#d_watershed) ) +- Allow multiple channels in the stack +- Add a dialog for the parameters +- Add interface to measure nucleus/cell parameters