Beads in May

some notes from AQLM

Friday, May 18, 2007

In short

This was the best AQLM ever.

Knowing biology is just as important as knowing physics in microscopy

We (the Blue Group) won the spectral conflict (or at least we had the most logical solution to the exercise)!!!! So as much as the physicists can leave us in the dust with their fancy calculations and physics know-how (I mean sometimes I cant even begin to understand the questions they ask in class), it is also important to know the biology.

Wednesday, May 16, 2007


It is well after midnight, and most of the data is recorded, and analysis is in high gear. The physicists are in their element, but the biologists are holding their ground.

We are very excited to see the solutions. The images are looking good....

High cheese/sleep ratio

Yes, it's true. A few of us watched the sun come up this morning, beers still in hand. There are some bad influences around here. You know John Murray is a good teacher when you can understand his lecture on 2 hours sleep.

One of us was punished for the visit to the attack by a statue of Mary. Or maybe the punishable offense was the shorts?

Swope, then and now...

We would be remiss if we didn't comment on the incredible changes at Swope.

A few years ago, the hydrophobic towels were replaced with the truly absorbent variety, which was a major improvement. Pushing water around your skin is kind of weird.

This year, the dining experience has been, well, transformed. Yes, the whole kitchen area is rebuilt. But the food! There is a selection, and it is in fact pretty good (ok, I have not tested any mayonnaise containing preparation-- maybe next year). Our regards and appreciation to all involved. Of course this has, in combination with the demands of quantitative approaches, substantially limited Phusion time. In the end, that is good.

A great transformation...

Spectral Conflict, in real time

The samples go out tonight, the results are in tomorrow.

John gave a beautiful lecture this AM on confocal and MP; the first slide for this afternoon starts addressing Poisson counting statistics. How could it get better?

Last night, a few of our esteemed staff went to church, then stayed up all night. Your faithful correspondent was of course safely tucked in bed by 1am...

Tuesday, May 15, 2007


after 4 Spaten, we have a question:
actually, we can't think of a question.

It's the night before the Spectral Conflict samples are handed out. the students are very concered about the competitive's scary.

The secret...

turns out the yellow group is already measuring camera offsets. Group spirit rocks.

Suck it!

What a cell biologist says to a biophysicist somewhere mid-Spectral Conflict....

Blinded by the light....

55 deg F. Tropical weather for sure....


Lasers abound...

First day of confocal, and everything is just humming along. John gave a nice description of SDCMs and Aaron's GFP lecture was clean as always. Whoever called Aaron mid-lecture-- just leave a message.

Color Wars

Last night there were some interesting late night discussions on how to make the course better. We are always looking for ways to improve the course, and we really do value the students opinions.

The spectral conflict was introduced this morning before Randi's ratio imaging lecture. Despite exhaustion and last minute preparation on the part of the faculty, I think we managed to get the message across as to what they should be measuring. This year we are introducing a new rule: for the evening spectral conflict session tomorrow night, data collection and analysis must end by 2am. The commercial faculty seem pleased, and who can blame them??

Monday, May 14, 2007

Spectrally Conflicted...

We've tested the samples, met with the vendors, written the lab, and now it's just a matter of chance.

Who will pair with whom?

Tuesday at 9am, it all begins....

Let the acronyms begin


Jason gave his usual stellar deconvolution lecture this afternoon, and handled the skeptical engineers and physicists very well. One gets the feeling that he's heard it all before.

We're all a bit more serious this year, planning all of these tedious quantitative exercises. I wonder if we will find time for a visit to the church yard...

The mythical Aaron Straight has arrived!


Today it gets real.

Rainer gave a great talk on TIRF, 4-Pi, STED, and PAM, all in the first hour of the morning. Decon comes this afternoon, then FLIM this evening.

And the mythical Aaron is supposed to beam in this PM.

We are now in overdrive....

Sunday, May 13, 2007

New Arrivals

Rainer, Mary-Ann, and Randi are all here now. The Mythical Aaron Straight is set to descend upon us tomorrow. Sadly, the "standard" microscopes in the main lab are being packed away as tomorrow we will begin to deal with out of focus fluorescence.

The heart of the course...

While the rapidly aging academics puff hot air, it's the course assistants that are making it all happen. Samples getting made, xeroxing, and group assignments and rotations... they ROCK!

Low Light Life

We've made it through all the camera lectures, and the students are now characterising all these fancy cameras. It's Sunday night, a bit late, and its a bit tricky with so many operators. but we are seeing some very nice measurements.

Spectral Conflict is looming....


We've managed to dim the lights and see the beads. t-tests were a bit tricky, but we are hopeful that the concepts are getting across....

Saturday, May 12, 2007

A conflict is brewing...

It's a beautiful sunny day in Woods Hole. Perfect conditions for sitting in a dark microscope room. The students are learning how to process images not just for beauty, but for quantitation as well.

Preparations for the spectral conflict are underway. Of course I cannot record here what we are doing, as it is top secret. But specimens are prepared, and John Murray and I will be doing some quantitation today to make sure we can get an answer that we can deem precise, and hopefully accurate as well.

Friday, May 11, 2007


the beads start tomorrow!!!!!

(thanks to wendy!)

DIC Lab Rocks!

We've seen collagen fibrils in furry little rodents, flagellar transport in clammy, and elodea....

It's Friday night and the lab's been full...I left my heart in sam clam's disco...

Fri Night

As the DIC lab buzzes in the background, the faculty are preparing for the more colorful part of the course...fluorescence. Details of labs are being sorted out, cells are expressing fluorescent proteins, and John Murray sits alone at the back of the lab looking at, what else? Beads.

On Error

During the discussion on error propagation, a student asked if calibrations made with the room lights off would work for meaurements made with the room lights on. David replied:

"In that case you are not doing an analysis of stochastic error, you are doing a stochastic analysis."

Thursday, May 10, 2007

A critical component!

We've discovered a critical component in the imaging light path: The Microscope! It turns out that this device is the major contributor to loss of photons in imaging. We will therefore remove this device from all further measurements requiring ultimate sensitivity.

Importantly, this was only discovered by careful, detailed, and of course, quantitative analysis.

Thurs Night

Champ is running around with his meter counting photons. Graphs are appearing on monitors. And Paul Goodwin is catching up on his email. Near 11pm and the students are still going strong. All in all, a good night. Tomorrow morning the error will begin to propagate.

Ted H. is, apparently, on a Rocky Mountain High.

Quantitative Lab #1

Tonight the kiddos are doing their step wedges. Our brains are already addled by Nacho Cheese Doritos and the Starburst (supplied by Molecular Devices-- thank you!). Washed down with Diet Coke and Amstel Light.

Heard in the lab-- "I don't mind being here-- I enjoy it!"

Down with AUs!

Dr. Swedlow has spoken. As is the new tradition, we hereby pledge to report all intensity measurements made at AQLM in photons.

Here we go again....

We're back live, at wonderful MBL. The fog has lifted, the scopes are out, and the students are learning Köhler....