A sneak preview of Volocity 4

Here in the lab, I’ve been lucky enough to have a sneak preview of Volocity 4.  I’d already heard that Volocity Classification has become Volocity Quantitation and from what I’ve seen so far it looks like the tools for making measurements have changed a lot. I thought I’d try Volocity Quantitation and report back on my findings.

I’m going to try using some data I’ve worked with before, just while I get the hang of this.

I’m going to see if I can obtain a value for the mean volume of the red structures in this data set. 

I’ve done this in Volocity 3.7 by using a classifier to identify the red structures and then measuring them.  There is no Classifier palette in Volocity 4 so I can’t use the classifier I made before, I’m told I can do everything I need to in the Measurements view, let’s have a look.

OK, the area marked 2 is just like the image view, in fact in the Measurements menu I have some of the same options that I have in the image view, like showing time or scale and changing between XYZ and extended focus.  That’s the view of the data I’ll need to make my measurements.

The area marked 3 is a list of all the tasks I might need to find my objects, I recognise most of these from the classifier and the area marked 1 says I need to ‘Drag tasks here to make measurements’.  Well then, I shall do just that.

When I used the Classifier I would start by thresholding by intensity.  Let’s see, ‘Find Objects by Intensity’, that could be it, I’ll drag that one in.

That’s got a histogram on it, I need to set this to the range of intensities I want to select.  There’s a tool tip that shows me what the values are.

Ooops that doesn’t look right.  Oh, I see, the task has a pop up to select the channel it works on, if I change that pop up from Green to Red and adjust the histogram that will be a step in the right direction.

It’s working on something, see the progress bar going across the screen? It’s finding a lot more objects than I expected.

Look at the list of measurements.  That’s what area 4 is for, it’s showing me some morphological and intensity measurements already.  If I click on the Volume column I can order the measurements by volume. I can now see why I’ve found so many objects, there are lots that are just a single voxel, that must be noise, I don’t want to select that.  There’s a task here to ‘Remove noise from selection’ so I’ll drag that in.

Yes, there we go that’s improving things but some of these selected areas look like more than one object. A different color is used to show where each object has been found and I see one color when I think there should be several objects. I’ll put ‘Separate Touching Objects’ in.  I can use the measurements so far to indicate the size of a single object to set the guide size for split objects.

That’s finding those objects well.  I can keep this protocol to use again by selecting ‘Save Protocol’ from the Measurements menu.

I actually want to keep these measurements and analyse them to find the mean volume so I’m going to select ‘Make Measurement Item’ from the Measurements menu. I’ve called this measurement item ‘Measured Objects’.

A Measurement item is a table of measurements which is in the library but separate from the image data.  This is different from Volocity 3, but it means that I can collect measurements from many different experiments together in one table and analyse them for patterns and trends.  That’s a bit beyond what I’m trying to do right now but is going to come in extremely useful in the future.

If I open the measurements item I can see a ‘Raw’ tab.  This contains the same data as I had in the table in the measurements view but they’re saved now and I can work with them further.

In the Analysis tab I use ‘Edit Analysis’ to set up how I want to rearrange this big table into something containing just the information I’m looking for.

So I’m looking at volumes, and I want the mean.  I want one mean for the whole data set so I’ll put the item name as the row.  And look I get one value. So now I can not only measure, I can analyse too!

This analysis dialog is also how I prepare data for creating most of the chart types available in Volocity, which is the next tab along.

I also tried opening an image sequence I stored some measurements with in Volocity 3.7 and I get an extra tab called ‘Legacy Measurements’, all the measurements I made in Volocity 3.7 are still safely in there.

Yes, I can see that Volocity Quantitation is different, but I already know how most of the tools work and I think it’s going to be a lot easier for other people around here to learn.  I can’t wait to see what new things I can do now.......