SutterPatch Walk-Through: #4 Data Navigator and Metadata

SutterPatch Walk-Through: #4 Data Navigator and Metadata

Now what I’m going to do is
I’ll run the “Bowtie_Test” here— which is scientifically completely meaningless— but this is a pretty useful waveform
for amplifier testing. For testing linear responses,
things like that. And this executes here. Let me start that a second time,
and I don’t even need to let that finish. I’ll just stop that. And then we’re going to go
to the Data Navigator. And here the Paradigm
that we just recorded includes four Routine Data sets, four Series. Two of the “My_IV” and two of the “Bowtie_Test.” And with the Paradigm highlighted
I can review the Paradigm Data, which gives me the two IV Routines and the one complete and
one manually stopped bowtie test Routines. This window, by the way,
this window behaves very similar to the Reanalysis Window that we saw earlier. We also got the Overview Navigator up here
that we can use to go back and forth, etc., etc… And if I highlight this one,
right-click on it, and go Analyze, it will open this Routine Data set,
this Series, in a Reanalysis Scope and now I can edit the Measurements, look at either last executed or the Measurements that were stored
with the original Routine. And as I run the analysis it recreates the real time analysis,
the IV that we plotted in real time, but obviously we can change the Measurements
if we want to look at something else. What we can also look at
is the Metadata. Let’s go to the Data Navigator
to do that. We have a bunch of Metadata
associated with this Paradigm here. We started the Paradigm
and here we have things like: We recorded this on a Mac,
which has a name, and with SutterPatch
version 2.0.3, build 214. A lot of these parameters. And then at one point we started a Routine.
The first Routine that we started— let me move over here— has a description of the individual signals
that were recorded, the serial number of the amplifier we used,
the revision of the amplifier, the firmware version.
Things like that. We have the series resistance,
the membrane capacitance, all the values that were stored when
I last closed the membrane test. And that all gets automatically determined. What I can do is I can add metadata to data
that I would record from here. So for example for the animal species:
in this case we want to record from mouse. And the animal age
could be, say, 6. And I purposely put a numerical value here
so I can make an age row or something like that, because my age units will be six days.
A young mouse that we recorded from. The tissue, for example, we would use brain,
and that would be a brain slice. We can create an identifier
that automatically increments by Experiment. For example, I could start counting at 17
and then increment that by 1 for each Experiment and can also get
a prompt confirmation before the Experiment. If I want to make sure I’m really recording from 17 today
and didn’t skip one that I don’t have there. And there’s a number
of parameters for the cells. If the parameters here aren’t enough
for you what you can do is… …in the Preferences you can
control the detail level. And let’s just quickly
look at the full details. I need to close this for
the changes to go into effect. So here we have more fields:
the operator, the experiment, the electrode, I mentioned that earlier,
for example, the pipette puller. If you have three pullers and one of them
always gives me smaller currents than the other one— which would be kind of odd—
you could track the serial number. You can add information about
the stimulus compound concentration, the compound lot,
things like that. Nobody would populate all six hundred
and some meta parameters that we have right now and then around midnight
start their experiments finally, but the idea is to give you
a structured place to store the data that you think is relevant for
your particular type of experiment. And then, yeah this here, the Metadata Review
is one way where you can see that. What else do we store with the Routine?
We’re looking at the Routine. A copy of the Routine that
we executed is also stored. And nobody wants to read
the text description of what’s going on but in most cases the waveform preview
gives you all the information that you need. Shows you okay, yeah,
this is what I did. And what you can do is you can
either copy that to your Routine Pool, or activate it
and run it as is. The benefit of that is
you can proliferate a Routine across multiple rigs
that you may have in your lab. Or you can reproduce what your
collaborator halfway around the world did. Or if you get unexpected results, and you want to make sure that you created
the routine so that it makes sense, I would ask you to send me
an Experiment file and then copy your Routine
to my routine pool, and that way I can run
the exact same Routine that you did, and can see, okay,
does this behave as expected? Did you make a mistake
setting it up? Which of course would never happen,
or at least I would never tell you. 😉 Or is it a bug
in the software? Which of course also doesn’t happen.
So this whole thing won’t happen. 😉 Anyway, we also have the analysis
associated with, in our case, the My IV. The IV curves.
You can look at that. And you can look at
the graphs or the table you can scale and add that,
append, average, etc., etc. One more thing I would
like to briefly talk about is how do we create an output—
like printable output—of my data. We analyze an individual Routine, zoom in on the the X axis a little bit,
because the currents aren’t particularly big, and then run the analysis—
run our IV analysis again— and then click on this little scroll here
which creates a Layout with my active windows. Let’s make that
a little bigger here. And what I can do then is
do a right click here, show this window, and this is a regular
Igor graph that I can modify. For example,
by double-clicking on the data I can select them all by holding
the shift key and making them all black, because it’s not likely that I want
to pay for a color figure for this here. You can obviously modify axis labels,
get rid of the grid lines, or something like that. Modify your figure as you
would be used to in Igor. Scale by using the scroll wheels here— the horizontal and vertical
scroll wheel in this case. And all this then
updates to the Layout. So you can create
your publication figures if you’re used to doing it
with Igor right within SutterPatch. One of the big advantages
of having SutterPatch within Igor. Follow along
the next episode in the series. Or jump to the playlist
for other informative videos. Subscribe now to keep up
with the latest installment.

Daniel Ostrander

Related Posts

Leave a Reply

Your email address will not be published. Required fields are marked *