Dr Vipoir Processes in Batches

More on Volocity 4 this month. I’ve discovered that batch processing has been implemented all over Volocity.  What this means is that I can now select a number of image sequences in my library and make changes and apply processing to them all, taking only one step to make each change.

It all works on the basis of channel names so I find it most useful for speeding up the jobs I need to do on sets of image sequences that are all part of the same experiment.  For example, I’m working with two fluorescent proteins at the moment and I always label the channels with the name of the protein, then each image sequence has a name which is made up of the date, the experiment number and details which tell me how the preparation was treated.

I would tell you more, but I’m a little way from publishing yet so if you don’t mind I’d rather leave it at that.

Batch processing, using the channel names so I can tell Volocity what to do, to which channels, in as many sequences as I like.  Cool!  Here’s three examples of what I’ve been up to.

First I select the sequences I want to work with in the library.

I can change the color look up tables applied to the each of the channels, I do each one in turn.

Straight to the tools menu and select “Change Colors…”

Choose the channel name to be changed and the look up table to apply.

All the channels with that name, no matter which image sequence they’re in are changed.  Channels that do not have that name will not be changed even if they do represent the same dye.

Back to the Tools menu “Change Colors…”Repeat the steps for the other channel.

I can perform Restoration by batch processing on all the channels in all the sequences.

As always with restoration I must have the correct point spread function for each channel.  Since point spread functions vary with features of the lens such as numerical aperture and refractive index of immersion medium I can only batch process sets of similar experiments.

With the image sequences selected I choose Fast Restoration… or Iterative Restoration… from the Tools menu.  Batch processing is the same for both.

Here’s the Iterative Restoration dialog:

The dialog lists the unique channel names found in all the image sequences.  Channels with the same name, even in different sequences, will be processed with the same PSF.

I assign the correct PSF to each channel, or check that Volocity has matched the names correctly.

Set it running and off I go.  I leave them to run overnight, the machine with the power for restoration really earns its keep this way.  The session log tells me how long the restoration of a particular data set took, so I can use that information to work out how many datasets I can run in an overnight session.

Batch processing also works for applying measurements protocols.  It requires a protocol to be saved after it’s created.

A useful tip when making the protocol, is that you can check how well it works on more than one image sequence without closing the measurements view.

Here I’m setting up the protocol in one of my sequences.

I can use the library navigation tools in the tool bar to move to another sequence in the library.

I select the sequence name from the list, only the sequences at the same level in the library as my first one are shown, or I move to the sequence above or the sequence below using the up and down arrows respectively.

The measurements view updates to show the new sequence and the protocol is automatically applied (I have Automatically Update Feedback turned on).

So having checked a few sequences (or not depending on the experiment) I select the sequences I want to apply this protocol to.  I select sequences in the library view.  I usually close the sequence I had open at this point - tidy screen, tidy mind.

Once the sequences are selected I choose “Measure” from the Tools menu.  I give a name to the measurement item that is going to contain all the measurements from all the sequences.

Each of the tasks that work on channels is listed in this dialog.  I just have to confirm the settings for each task.  Once set I click OK and off it goes.

Each task in the protocol is applied to each timepoint in each sequence.

I like to go for a cup of tea at this point, milk, four sugars.  Splendid!

Suitably refreshed I’m ready to look for trends and patterns in this data, but that, my friends, is next month’s story.