Takes a Nikon ND2 file and visualizes it lazily in BigDataViewer #BIOP #Fiji #BigDataViewer #NikonStereology

NikonStereologyBdvVisualizer.groovy

// You need to activate https://biop.epfl.ch/Fiji-Bdv-Playground/  for this script to function
// It takes a Nikon ND2 file and Visualizes it lazily in BigDataViewer, also opens some windows to control Brightness
// Of each channel present in the file
// Nicolas Chiaruttini, BIOP, EPFL, 2021

#@CommandService cs

#@SourceAndConverterService sac_service

#@File(label="Select your Nikon ND2 file (single timepoint only)", style="open") nikonNd2File

// Opens Nikon nd2 dataset ( = multi series )
def dataset = cs.run(BasicOpenFilesWithBigdataviewerBioformatsBridgeCommand.class, true,
	"unit", "MICROMETER",
	"files", [nikonNd2File] as File[],
	"splitRGBChannels", false
).get().getOutput("spimData")

// Sets a meaningful name to the opened dataset - if not it is called SpimData 0
sac_service.setSpimDataName(dataset, nikonNd2File.getName())

// Uses the Bdv UI to fetch the number of series ( how many nodes are there below dataset>SeriesNumber ?
//def datasetPath = sac_service.getUI().getTreePathFromString(nikonNd2File.getName()+">SeriesNumber")
//def int number_of_channels = datasetPath.getLastPathComponent().getChildCount();

cs.run(BdvSourcesShowCommand.class, true, 
	"autoContrast",false,
	"adjustViewOnSource",true,
	"is2D",false,
	"windowTitle",nikonNd2File.getName(),
	"interpolate",false,
	"nTimepoints",1,
	"projector","Average Projector",
	"sacs", nikonNd2File.getName()).get()

cs.run(BasicTransformerCommand.class, true,
	"type","Flip",
	"axis","Y",
	"timepoint",0,
	"globalChange",false,
	"sources_in", nikonNd2File.getName()
).get()


cs.run(BasicTransformerCommand.class, true,
	"type","Flip",
	"axis","X",
	"timepoint",0,
	"globalChange",false,
	"sources_in", nikonNd2File.getName()
).get()


// Uses the Bdv UI to fetch the number of channels ( how many nodes are there below dataset>Channel ?
def datasetPath = sac_service.getUI().getTreePathFromString(nikonNd2File.getName()+">Channel")
def int number_of_channels = datasetPath.getLastPathComponent().getChildCount();

for (int index_channel=0;index_channel<number_of_channels;index_channel++) {
	cs.run(BrightnessAdjusterCommand.class, true,
		"sources", nikonNd2File.getName()+">Channel>"+index_channel);
}


import ch.epfl.biop.bdv.bioformats.command.BasicOpenFilesWithBigdataviewerBioformatsBridgeCommand
import sc.fiji.bdvpg.scijava.command.source.SourcesRemoverCommand
import ch.epfl.biop.bdv.command.exporter.ExportToImagePlusCommand
import ij.plugin.Scaler
import ij.plugin.ZProjector
import ij.IJ
import org.apache.commons.io.FilenameUtils
import ch.epfl.biop.bdv.bioformats.imageloader.SeriesNumber
import groovyx.gpars.GParsExecutorsPool

import sc.fiji.bdvpg.scijava.command.bdv.BdvSourcesShowCommand
import sc.fiji.bdvpg.scijava.command.source.BasicTransformerCommand
import sc.fiji.bdvpg.scijava.command.source.BrightnessAdjusterCommand