Does anyone have an efficient way to calculate maximum intensity projections for every position
in a multiposition acquisition from Micro-manager? We're acquiring some large multiposition
Z-stacks (100s - 1000s of positions) and would like to calculate the maximum intensity projection
along Z for subsequent stitching.
I currently use the following beanshell script, which works, but is quite slow, and I feel there
must be a faster way to do this. I suspect the problem is in the way I'm calling the imageJ
functions, but I'm not sure what would be faster. The calls to the gui object are Micro-manager calls.
Thanks,
Kurt
The script:
import ij.IJ;
acquisitionName = gui.openAcquisitionData("D:\\Test_grid_Z\\test_4",
false, true);
acquisition = gui.getAcquisition(acquisitionName);
acqWindow = acquisition.getAcquisitionWindow();
nPos = acqWindow.getNumPositions();
gui.message("Total " + nPos + " positions");
for (int pos = 0; pos < nPos; pos++){
acqWindow.setPosition(pos);
IJ.run("Z Project...", "start=1 stop=21 projection=[Min Intensity]");
IJ.saveAs("Tiff", "D:\\Test_grid_Z\\test_4_MIN\\img_" + pos + ".tif");
IJ.run("Close", "");
}
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html
Locked
