Hi Patrick - in ImageJ1 you should be able to use the Measure->Analyze particles tool, to get measurements.
You could also look into some of the ImageJ2 scripts. In the script editor under Templates->Turorials there is a script called “Ops Threshold Measure”. This goes over some of the steps you would take to measure structure in an image. It is only a template, so it won’t work perfectly on your data, you would have to learn a bit about ops and optimize the steps for your images.
If you have time constraints, you may want to just concentrate on learning about the IJ1 options for measurement (https://imagej.nih.gov/ij/docs/guide/146-30.html). If you have the time I’d highly recommend trying to write a script using ImageJ2/ops.
As a side note the “Ops Threshold Measure” script currently measures objects, but does not generate an output table. I think I noticed some people working on tables lately, is there an easy way to modify the script so the final object measurements appear in an output table??
# @OpService ops
# @ImgPlus inputData
# @Double sigma
# @OUTPUT ImgPlus logFiltered
# @OUTPUT ImgPlus thresholded
# @OUTPUT ImgPlus labelingIndex
# Run this tutorial using the C0Z12 image generated in the 'Crop Confocal Series' tutorial.
# To generate the C0Z12 image, do the following:
# Go to 'file>Open Samples>Confocal Series' and make sure confocal-series.tif is the active image and
# run the Crop Confocal Series tutorial.
from net.imglib2.algorithm.labeling.ConnectedComponents import StructuringElement
from net.imglib2.roi import Regions;
from net.imglib2.roi.labeling import LabelRegions;
# create a log kernel
# otsu threshold and display
thresholded = ops.threshold().otsu(logFiltered)
# call connected components to label each connected region
# get the index image (each object will have a unique gray level)
# get the collection of regions and loop through them
for region in regions:
for region in regions_big:
# get the size of the region
# get the intensity by "sampling" the intensity of the input image at the region pixels