Strike that....substitute silence.

Dear all,

I have made a mistake, and perhaps led you all astray.

It is true that in the Axopatch, the signal ground is not connected to the power ground.

But, it turns out that it's very difficult to isolate power ground from signal ground, without essentially breaking every BNC connection between the amplifier and the digitizer. And when I did that, I got a good amount of hum pickup from those now unshielded wires. At times you could find a position where the pickup was minimal, but it wasn't easy. And figure that you've got at least 3 connections at a minimum (signal output, analog input, and gain), that all equals one big pain in the butt.

This advice originated when the digitizers were the old Digidata 1200. That digitizer is specifically designed to isolate the signal ground from the power ground (most important to isolate it from the computer, whose fast switching power supply is a huge noisemaker). That all changed in the 1300 line of Digidatas.

However, it does seem that the simple act of using the grounded to non grounded plug adapter on the amplifier, does dramatically reduce the RMS noise level. Why it exactly does this, when there's still a connection between signal ground and power ground, I am not clear on.

Nevertheless, I am available to come and lay my hands on your setups, to reduce the noise. Cause it seems I'm back to that level of rationality for this whole process.

Gotta bring this up with the big guy soon.

Geek alert

I might just be in productivity nerd heaven:

Liquid Planner added task timers!

Now I can reach new levels of accuracy in tracking blogly time wasting.

A Tale of Two Grounds

It was the best of rigs, it was the worst of rigs,

It was the age of 0.07 pA RMS, it was the age of 0.5 pA RMS, ±5 pA p-p at 60 Hz,

It was the epoch of separating signal ground from power ground, it was the epoch of connecting all power grounds to the signal ground,

It was one really annoying run on sentence written by some old white dude, it was a kick ass blog post written by a middle aged white d00d.

There's one thing I've learned here as postdoc that I've actually never seen discussed in other places. When I first heard it, I did a "Watch you talkin' about" head turn, thinking it was crazy.

That thing is, to get really good noise on your patch clamp rig (good meaning low here), you can make 2 grounds. One ground connects everything that is physically close to the headstage. This gets connected to the signal ground plug. The second ground connects everything else. That gets connected to power ground.

Figure 1: Nat's newly refurbished set up (which is tight if I do say so myself). Axopatch 200B and Sutter MP-285. Green As indicate things attached to signal ground. Magenta Bs are connected to power ground.

So what goes on the signal ground?

• Microscope
• chamber
• condenser
• bent piece of metal that can be put right in front of headstage/chamber to further shield (not shown)

That all gets connected to the gold pin at the back of the headstage (or equivalently at the signal ground input on the back of the amplifier). Note that you'll need to break the power ground connection (with a 3 to 2 adaptor). Doing this will get you most of the way there.

What goes on power ground?

• Faraday cage
• air table surface
• manipulator

This is connected to power ground (either attach it to an exposed copper pipe or to power ground through the case of the manipulator). Doing this will get you to the super low RMS values specified in teh Axon manual.

Now I no longer fear denoiseing the setup.

The only tricky things I've run into are that most of the BNC inputs on the Digidata are connected to power ground. So usually I have to break the ground connection to connect the gain value output from the amplifier to the digitizer input (I've never had the amplifier signal output to digitizer analog in cause this).

I just turned on my amplifier, and with a pipette holder on, the PATCH mode RMS noise is 0.099, and WHOLE-CELL mode is 0.48. SHU-WEET!

What have I, what have I, what have I done to deserve this?

When your electrophysiology rig has only a single BNC cable connecting the patch clamp output to the digitizer, you know things aren't good.

Especially when there's still a little 60 Hz ripple visible.

And when you still haven't solved the periodic pipette vibration that makes getting seals hard.

[Then after you write some schlock like this, you worry about what PLS thinks about it.]

In other news, I have discovered a couple things:

When there is 0.5 pA RMS noise on a well shielded headstage, cleaning where the holder attaches can do wonders. Isopropanol + canned air = 0.05 pA RMS.

When ultrasonic cleaners are used correctly, they kick total ass. If you have one, try the glass slide test. HOLYMOLYCOWTHATISCOOLANDSADLYMIGHTBETHEWEEK'SHIGHLIGHT!

InaDWriMo2009 - do it, do it now!

As if it weren't patently obvious, I'm still swamped under the combination of multiple projects, multiple collaborations, and multiple offspring. I just haven't hit upon a way to incorporate much blogging.

One of the other things languishing is a couple of projects in different stages of writing. One is a manuscript revision that has been in periodic hibernation since I left my thesis lab. (Ok, it is embarrassing to write that. The reasons for such a state might be both understandable and inexcusable, but at this point, who cares? It's time to get it done). This requires a substantial rewrite of the Discussion section, as well as the Introduction. This also requires some time with the literature, which I have been only peripherally following once this project came off the front burner.

Another writing project is a draft of a short manuscript, on some old results that started fast and then got stuck in neutral. While this project isn't completed, I think I know enough of the general story to at least start a draft. Writing that will make it much more obvious what needs to be done in order to publish it.

To help motivate me, I've decided to join up with the InaDWriMo2009 that Dr. Brazen Hussy is hosting. It's derived from a dissertation specific "fork" of the NaNoWriMo, that has been extended to all sorts of academic writing projects.

I figure that combined, the both of these will require something on the order of 5000 words. My goal is to complete them during the month of November. Watch the side bar for progress.

And, who else is in? The motivation is contagious. Sorta like H1N1, but with mental pain rather than physical.

Shallow thoughts

Sometimes I feel like experiments are performance art with no audience.

Blogrolling, Junction Potential Style!

I recently started following Jerry Coyne's blog over at "Why Evolution Is True"and I wanted to highlight it in case it flew under other folks's radars. Jerry is a prominent evolutionary biologist, and is well known for his critiques of intelligent design and other creationist gobbledygook. His essay, "The Case Against Intelligent Design: The Faith that Dare Not Speak Its Name" (here) is required reading for anyone interested in the subject.

Today's issue of Science has Jerry's review (sorry, behind paywall) of Chris Mooney and Sheril Kirschenbaum's book Unscientific America. It's definitely worth a read (check back at WEIT, as he might be able to post more of the review there), though a little more shrillness would help. ;)

Now, I'll admit I'm somewhat partial here, seeing as Jerry teaches at the University of Chicago (oh, dear alma mater). In fact he taught the required evolutionary biology class back in 1995 when I was but a larval biologist. Sadly though, at the time I was a fairly uninspired student of the subject, making me wish I could do it over again now. Maybe in another life.