Identify and measure objects in an image document.

Hello and welcome to another tip of the month!

You may know that I opened the User Forum, Dr Vipoir's on line Surgery, last month. You can use it to contact me about your Improvision software questions any time you like. I thought it would be useful to use one of the queries posted on the Forum as the basis for my tip this month, as it is a subject that will be of interest and benefit to many of my patients.

The query was about how to identify and measure objects in an image document. To do this in Openlab you need to have the Morphology Bundle of modules, which includes Density Slicing and Advanced Measurements.

Below I will show you how to use Density Slicing to measure the DAPI labeled nuclei in this image document.

First draw a region(s) of interest within the area that you want to identify.

Remember if you need to draw more that one ROI hold down the shift key as you are drawing.

Now go to the Image menu and select Density Slice…

Select the color model to be used:-

If you want my opinion use the H S I model as it is generally easier to use.

Then click on the Grab from ROI button.

This will set those three slider bars in the dialog to the range of values present in your ROIs. Next adjust the sliders until the preview is to your satisfaction, i.e. the colored areas are marking all the objects that you need to be selected. If you need to take a closer look select the crop preview.

Adding a transparent tint might be to your liking, it might make the objects easier to identify in the preview, this will not affect the final image it is only for the preview.

Click on the slice button to create a binary layer which shows the objects that have been identified within the thresholds that you have set.

Here is the slice:

Next to measure the objects.

Open the measurements windows from the Image menu … Show measurements

Go to the Measure drop down menu on the table and select measure objects.

We will measure the objects using as a mask the binary layer created by density slicing the image. This will produce a range of measurements including useful intensity measurements from the image document.

When you are ready to go click on the Measure button.

Hey presto here are your measurements, which appear in the measurements table.

Objects can also be selected and measured using Volocity. Have a look at this i-Tip that covers the use of the Classifier in Volocity.

If you've got any questions let me know by posting your query on the Forum.