DEVELOPERS

Developer notes for extending KiT
=================================

Updated: December 2015.

If you extend KiT, please consider submitting your code to the BitBucket
repository http://bitbucket.org/jarmond/kit.

Implementing new particle/spot detection and/or refinement algorithms
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The choice of detection algorithm is controlled by jobset.options.spotMode, and
refinment algorithm by jobset.opitions.refineMode, each of which is a cell array
of strings, one for each channel.

New particle detection algorithms can be added to kitFindCoords.m under the
switch spotMode construct. Refinement algorithms can be added under the switch
refineMode construct. Please see the existing algorithms, e.g. 'histcut',
'centroid' for usage,

The detection algorithm is required to return a cell array with nFrames
elements. Each element is a nx3 matrix of n particles.

The refinement algorithm is takes a job struct and returns a job struct with the
refined particle locations. The job struct contains a cell array field
'dataStruct', one element for each channel. For the current channel the
refinement algorithm must return the job struct with the
dataStruct{channe}.initCoord struct added. The initCoord struct consists of the following fields:
  .localMaxima : the original detected particle locations.
  .allCoord: the refined particle locations in um.
  .allCoordPix: the above in pixel coordinates.
  .amp: the amplitude (e.g., signal intensity) of the particles.
The struct has one element per frame. See kitCentroid.m as an example.


If a new algorithm requires options, these can be added to
kitDefaultOptions.m. This will cause them to be added to the jobset.options
struct whenever kitRunJobs or kitGUI is called. To enable display in the GUI,
appropriate strings should be added to the cell array maps at the start of
kitGUI.m