Upgrading to Volocity 5

I am very excited today because I have just had my first play with our newly upgraded Volocity 5 software. It has a completely redesigned interface which I was able to get to grips with very quickly and I can see that it is going to make my life a lot easier!

The first thing I noticed is that a new user gets a lot more assistance about what to do when they first open Volocity with the large, clear hint on first starting Volocity.

Volocity 5 upgrade

On the acquisition systems connected to the microscopes there are really obvious shortcuts to the video previews.

When I opened up my library, I noticed straightaway that the library view has changed. Now I can see a thumbnail for each of my image sequences, making it much easier for me to distinguish between different experiments.

The library view in Volocity

Volocity 5 library view

Another feature that helps pin-point the correct data set more quickly now is the descriptive text under the thumbnail. This provides me with information about the item in the library. For image sequences, this shows the size of the sequence; X, Y and Z dimensions, number of time points and number of channels. This is going to come in very handy as several of my thumbnails look quite similar.

Image thumbnails

The new library view in Volocity 5

In Volocity 4, I had to double click on the library item to open up my desired data set. However, in Volocity 5 I only have to click once on the library item to show it in the same window, if I decide I’d rather see a different item then I select that one instead. I can streamline my work by only ever having one window open. This doesn’t suit all the tasks I perform with Volocity so I still use the ability to double click an item to show that data in its own, separate window. I can still have multiple windows open at once and open the same data set multiple times.

Library view

Double clicking on your library item in Volocity 5 will open up your image in a new window.

We’ve all noticed that even when we’ve got a license for Volocity Visualization, some tabs have been removed.

image view in Volocity 4

In Volocity 5 the image view is our ‘one stop shop’ for different ways of representing our data and this reorganization has given us some pretty cool new capabilities. We see what these are when we look at the Mode pop-up in the tool bar, or select Mode from the Image menu, for a 3D data set.

The drop-down toolbar in Volocity 5 provides different options for viewing your data

Library view volocity 5

The modes we’re familiar with are still there, XYZ, the four part orthogonal view and the extended focus, but now we can also work with the individual parts of the XYZ view.

Volocity 5 xyz

I can now choose to just view the XY, XZ or YZ planes. I would imagine that I might find this useful if I just wanted to capture a snapshot of one particular plane for a talk, or to illustrate a point in a paper.

Volocity 5 planes

Or I can view the 3D planes; the rotatable object from the top left of the XYZ view which shows how the X, Y and Z planes interact.

Volocity 5 3D planes

When Volocity Visualization is licensed on the system the 3D rendering options are available. 3D Opacity is the new name for the HR Opacity Renderer. The HR Intensity renderer has not been removed but now it is an option which can be set for individual channels. Choose Max Intensity from the pop-up in the channel control. We find some data sets are better illustrated with Max Intensity rendering, it’s really great to now be able to mix this with the opacity renderer, we’re going to be able to illustrate our findings even more effectively.

Volocity 5 rendering view

Speaking of the 3D Opacity renderer, my PhD students tell me about how they use a joystick to navigate through the volume, just like they would in a game console! I had no idea that you could do this- did you?

The Ray Tracer, as it was called in Volocity 4, is now called the 3D Ray Tracer. I must admit that this is not something that I regularly use, but my colleague down the corridor loves it and she uses it to make some stunning images for publication.

This single image view has one more trick, those of us that are particularly eagle eyed notice that bookmarks and the movie making interface can be shown for the image view, regardless of which mode it is in.

Volocity 5 single image view

This means that we can use these tools for storing the appearance of the view and animating transitions in all the modes. There are movies showing a step through of the YZ plane or the slice view coming off our systems all the time now. Coupled with the ability to splice or tile image sequences our presentations are taking on a whole new dimension.

Something that I really like about the XYZ view is that if I click on the Inspect tool to locate a specific point within each of my planes, I am now given the co-ordinates of that point in X, Y and Z. I have already found a use for this - one of my technicians was trying to explain to me via email that there was a small dense patch on one of our images that looked like it might warrant further investigation, but rather than have to explain in detail where it is, she simply said “it is at point [X: 19 Y: 32 Z: 103]”, how easy was that!

Volocity 5 x, y, z co-ordinates

The XYZ Planes view in Volocity 5 showing the X, Y and Z co-ordinates

In keeping with the theme of tidier windows there is no navigation palette in Volocity 5. I use the navigation palette to control how channels appear in each view and to navigate through time-resolved data; I have it open on my screen all the time. Now these controls are part of the view.

Volocity 5 channels view

I alter how the channels appear in the view or hide them completely using the channel controls on the right and I navigate time using the controls at the bottom. When I want more space for the image and I’m not using these controls I can hide them using the options in the image menu.

Volocity 5 hiding controls

In Volocity 5 the navigation controls are now incorporated into the Image menu.

I am given the option of choosing to view the channel controls, the time navigation controls, the movie controls, and the bookmark pane.

Yes I can definitely see that Volocity 5 is going to make my life a lot easier, and it will enable me to be a lot more productive.

Have fun playing with Volocity 5!