Micro-Manager script to uploading image sequence to Andor Mosaic3 using core API.

mosaicSetupSpeckleAcquisition.bsh

// Upload image from stack to SLM before each frame in MDA.
//
// We have to use the core API to upload each frame individually,
// since there is no public sequencing API for SLM devices.
//
// Pariksheet Nanda <pariksheet.nanda@uconn.edu> July 2014
//
// License: Public Domain

import ij.io.Opener; // To load TIFF stack file from disk.
import ij.ImagePlus; // To hold the opened image.
import ij.ImageStack; // To access stack pixels.

// Load file from disk.
Opener opener = new Opener();
ImagePlus imp = opener.openImage("C:/Users/Andor/Downloads/speckle.tif");

// Get stack info.
ImageStack stack = imp.getImageStack();
slices = stack.getSize();

// Set MDA to acquire the number of slices.
seqSettings = gui.getAcquisitionSettings();
seqSettings.numFrames = slices;
gui.setAcquisitionSettings(seqSettings);

// Get the installed name of the SLM.
mosaic = mmc.getSLMDevice();

// Boilerplate when using runnables.
gui.clearRunnables();

// Runnable to upload each image to the SLM.
runnable = new Runnable() {
      int slice = 1;
      
      public void run() {
	 // Get the pixels of the stack slice.
	 pixels = stack.getPixels(slice);
	 // Upload the image to the SLM.
	 mmc.setSLMImage(mosaic, pixels);
	 // Activate the uploaded image on the SLM.
	 mmc.displaySLMImage(mosaic);
	 print("Activated slice " + slice);
	 slice++;
      }
   };

// Dimension order is frame, position, channel, slice.
gui.attachRunnable(-1, -1, -1, -1, runnable);