An example script to show how to filter spots after the detection. #Fiji #EasyXT-Fiji #Imaris #BIOP

ijs-EasyXT-Filter_detectedSpots.groovy

name_spots = "pinkySpots";
name_filtered_spots = name_spots+"-filtered";

rt = new ResultsTable()
rt.reset()

// Here teh script expect to find the demo.ims file in the folder Fiji>Plugins>BIOP
def plugins_dir = IJ.getDirectory("plugins")
def biop_dir = new File(plugins_dir , "BIOP")
ims_name = "HeLa_H2B-mcherry_Tubline-EGFP_mitochondria-MitoTracker_reduced.ims"
ims_path = new File( biop_dir, ims_name)

// get ImarisApp
def imaris_app 		= EasyXT.getImaris()
// make Imaris open an imaris file 
EasyXT.openImage(ims_path)

//we detect the spots and add them to the Scene
detected_spots = SpotsDetector.Channel(2)// 3rd channel
	                    .setName(name_spots)
	                    .setDiameter(3)
	                    .setFilter("\"Quality\" above 25")
	                    .isSubtractBackground(true) 
	                    .build()
	                    .detect()	                    
EasyXT.addToScene(detected_spots)                    

// get the number of spots
detected_spots_Nbr = detected_spots.Get().mIds.size()

// prepare lists to store required infos to create spots
def xyzFiltered_spots 	= []
def tFiltered_spots 	= []
def rFiltered_spots 	= []

for ( i in 0..detected_spots_Nbr-1){
	// with this silly example , we check if it belongs to an even (or odd) time-point ? 
	if (detected_spots.Get().mIndicesT[i]%2 == 0){
		// and add 
		xyzFiltered_spots.add(detected_spots.Get().mPositionsXYZ[i]) 	// alternatively : detected_spots.GetPositionsXYZ()
		tFiltered_spots.add(detected_spots.Get().mIndicesT[i])			// alternatively : detected_spots.GetIndicesT()
		rFiltered_spots.add(detected_spots.Get().mRadii[i]) 			// alternatively : detected_spots.GetRadii ()
	}
}

//make new spots, using the IFactory
filtered_spots = imaris_app.GetFactory().CreateSpots()
// assign the required information for the spots
filtered_spots.Set(xyzFiltered_spots as float[][] ,tFiltered_spots as int[] ,rFiltered_spots as float[] )
// (optionnal set a name)
filtered_spots.SetName("Filtered Spots")
// add to the scene
EasyXT.addToScene(filtered_spots)


/*
 * A more advanced filtering using results from Statistics
 */
spots_id = detected_spots.GetIds()
rt = EasyXT.getStatistics(detected_spots, "Intensity Median") // get a table with value for all the channels
//rt = EasyXT.getStatistics(detected_spots, "Volume") // 
//rt.show()


def xyzAdvFiltered_spots= []
def tAdvFiltered_spots 	= []
def rAdvFiltered_spots 	= []
for ( i in 0..detected_spots_Nbr-1){
	// with this silly example , we check if it belongs to an even (or odd) time-point ? 
	
	id_row =  getRowIdxOf ( rt , "ID" , spots_id[i] )
	median_int_C3 = rt.getValue("Intensity Median C3", id_row)
	
	if ( median_int_C3 > 100){
		// and add 
		xyzAdvFiltered_spots.add(detected_spots.Get().mPositionsXYZ[i]) // alternatively : detected_spots.GetPositionsXYZ()
		tAdvFiltered_spots.add(detected_spots.Get().mIndicesT[i])		// alternatively : detected_spots.GetIndicesT()
		rAdvFiltered_spots.add(detected_spots.Get().mRadii[i]) 			// alternatively : detected_spots.GetRadii ()
	}
}

//make new spots, using the IFactory
advFiltered_spots = imaris_app.GetFactory().CreateSpots()
// assign the required information for the spots
advFiltered_spots.Set(xyzAdvFiltered_spots as float[][] ,tAdvFiltered_spots as int[] ,rAdvFiltered_spots as float[] )
// (optionnal set a name)
advFiltered_spots.SetName("Adv. Filtered Spots")
// add to the scene
EasyXT.addToScene(advFiltered_spots)



/*
 * Companion function to look for an ID in the result table
 */
def getRowIdxOf ( ResultsTable , ColumnName , UniqueID ){
	row = 0
	while ( row < rt.size() ) {
		if ( rt.getValue(ColumnName,  row) == UniqueID)	return row
		else row++
	}
}



return


import Imaris.*

import ch.epfl.biop.imaris.*

import ij.*;
import ij.measure.ResultsTable