Beads in May

some notes from AQLM

Thursday, May 25, 2006

AQLM in Repose

It's been about two weeks since the Spectral Conflict Finale and the whole AQLM experience. I suspect something special happened this year-- it seems a combined effort of both faculty and students produced something more, something new. We have a few emails from students, and even a couple from faculty that state this in various ways. Interestingly, noone articulates it perfectly-- as if we did something that we can't quite fathom.

We really tried really come to grips with quantitation in a microscope. Obviously, we didn't succeed-- it's just too hard to do so in a course with a limited period of time. But we made progress, and all seem to recognize that a joint effort was worth it and amounts to a significant achievement.

We also made a step along a path we've all discussed for some time-- a remodeling of a course that necessarily must address a very long and important history, but that also must include new methods, techniques, and approaches that are driving the field forward, and frankly, keep us passionately dedicated to this pursuit. This is a natural, probably unresolvable tension.

We're not there yet, and we are still defining where there is, but we are on our way.

Saturday, May 13, 2006

Is it wrong to miss aqlm quantitative exercises? Thanks for the course guys.

-P. Cavnar

The End

AQLM is like the wind. It comes and it goes. Last Thursday the lab was filled with microscopes, and now there are not even boxes left.

Thanks to all for a great course, especially the students.

And watch the winners of the "Student Most Likely to go into Fourier Space Award." We shall hear from them again.


Friday, May 12, 2006

Last Night

It was a very good set of presentations, and even included a couple examples of error propagation. Dinner included micro-sectioned beef and lobster. All OK. There is a nice sense of calm about the course. We've done well.

Thursday, May 11, 2006

The Grand Finale

We are minutes away from the end of Spectral Conflict. Furious drawing and plotting of graphs, and reviewing all of our previous lectures and exercises. It's been two days of hard work and passion. Some raw nerves, but we are looking forward to some great solutions. Off to Whitman!!!!

The Maggot

Today is GFP day, so the maggots are out in full force. Instead of the usual maggot award, Aaron and Ted will be collecting images for a maggot "art project". In addition, the students were instructed to measure anything they would like about the maggot in true cell biologist form...that is, measure once with no statistics.

The conflict continues

The students looked pretty worn out as they trickled into Aaron's GFP lecture this morning. Last night went pretty late. Jason and I visited each group between 12:30-1:30am and many were still going strong. I saw some nice calibration curves, so we are hopeful that there will be good solutions presented this afternoon.

Wednesday, May 10, 2006


We all headed to Phusion tonight for dinner, only to find that Carol's chef quit this morning. We were forced to eat fried seafood at the LandFill. On the way back to the lab, Jason, Ted, Aaron & I stopped in to console Carol over wine and cheesecake.

The students are working away at their quantitative exercises. We've already been asked for good controls by two of the groups, so our expectations for quality results are on the rise.


This is not...

Arbitrary and Qualitative Lite Microscopy

Pinholes everywhere

Today is confocal day...the day John Murray works his butt off while the rest of the faculty catch up on sleep. Tonight: Phusion!

The man and the myth

Aaron Straight was spotted at 12:47pm EDT in the foyer of Swope. The next burning many hours will he stay?

Tuesday, May 09, 2006

A box and a myth

A box arrived today from the Mythical Aaron Straight. Will he show up?? We have started a pool guessing how many hours before his lecture he will step off the Bonanza bus.

It's raining

Really Ted. It's raining, it's pouring. It's cold. We're in New England in May for God's sake. Take off the damn shorts.

Time Lapse

That's flimsy.

Phase modulated what?

We think phase modulated widefield fluorescence lifetime imaging may have worked. Then again, maybe not. But after some whisky and discussion we are convinced that one day it will. Pretty cool stuff.

Deep Thoughts by Dee

We live in the time domain, and that's why we do timelapse microscopy. If we lived in the frequency domain, we would do FLIM.

Snacks for Scientists

Smartfood: Physics in a bag

Rainer's Lecture

Rainer's comment that one should never average calculated values has created a serious bias among the students. It is causing them to "cry scared!"

Autoquant's Premature Departure

Autoquant has left us to go whereever it is that image processing companies go, leaving Greg and the Red Group in the lurch. Were they driven away by fear of the Spectral Conflict? Happily Red Group has now been adopted by MediaCybernetics.

We've lost Jennifer...

It's a sad day...

Jennifer: "I'm saving myself for Swope."

We've lost her.


...might be a night for the water of life.

Decon Lab....Done!

Made it to Tuesday afternoon, and we have happy students with beautiful PSFs and some very nice images from Jennifer's slides. The mitotic spindle is just more beautiful than any other part of the cell....

The Spectral Conflict

This morning we handed out the spectral conflict exercises and the groups were chosen. It almost broke my heart to see the students smiling as they chose their vendor partners and chatted about their approach. They have no idea what they are in for. John and I had to do some troubleshooting to get the specimens just right. Turns out I do remember how to pipette a serial dilution.


Vectashield is evil and must be destroyed.


Our dear friend Carol, the owner of Phusion, has agreed to open for us on Wed we can have one more real meal before the banquet.



After much effort, we finally made FRET happen. Phew!


The looming banquet

Our dream of having the banquet at Phusion has been dashed. Maybe next year...

Them darn pixels....

Spent the day measuring pixels (aaaaaaargh!) and the evening doing lifetimes. Mary-Ann gave the clearest description of fluorescence lifetime in memory.

The Spectral Confict samples are ready...let the games begin.

Monday, May 08, 2006

Pretty pictures

Pretty pictures will get you on the cover of the Rolling Stone ... quality data will get you on the cover of Science.

- The Unknown Imaging Comic

Sunday, May 07, 2006


"You are always linear. On the other hand, you are never linear."

David Wolf, Fluorescence lecture

Turn off the lights

It's Sunday, and things are about to get a lot more colorful...


Quantitative Lab #2

We've got through the second quantitative lab, plus a full day of Pol and DIC. Everyone's doing pretty well, and most peope are picking up the idea of making the measurements. Ted S. was amazing, as usual. And tonight, the first departures to Phusion; might start being a trend...

Saturday, May 06, 2006

Jason and I have discovered, quite by accident, an unbleachable form of YFP. The paper will be submitted to Nature by the end of the course.


We are making an ionomycin stock solution without permission. Let the games begin.


The answers are out there.

I just googled "How many photons per electron?". There were 3,160,000 hits.


Ted H. is looking at sperm with DIC. Disgusting.


Polarized Light!

It's the polarization and DIC day. Ted Salmon is dutifully splitting the light rays, and doing the dance.

Last night was our first of six Quantitative Labs. Went OK-- some nice photon plots showing (what we think) is linear response in scientific grade CCDs... Whopeeeeee! We are all learning

Ted H. thinks most of the answers for the course are on Ask Jeeves... Hmmmmmmm

Friday, May 05, 2006

The First Quantitative

We are Off-- the first Quantitative Lab!!!!

(and a broken water main!)

How many photons?

At AQLM, we pledge to publish all measurements in photons. For a CCD detector:

Number of electrons = [full well capacity/(max greyscale-offset)]*(greyscale value-offset)

Number of photons = Number of electrons * (%QE/100)

Don't Fear the Bead

Hey, welcome to the AQLM Blog. Thoughts, notes, wishes, contemplations, requests for Ted to change his shirt...anything at all.

We will begin with a poem.....

When they began to pump Swope’s septic,
It made me utterly dyspeptic.
My stomach slid down a slippery slope,
Induced by Swope; confused by Swope, gone is all hope.
Indigestive cramps consumed my day
With pains that even Pepto won’t alay.
Such agony, I think, is now my lot.
It is pink, but I am not. I have forgot
Microscopy, now distant memory,
As are fluorescence and probe chemistry.
Cameras seem chimeras, confocals vocals.
Is this some feverish delusion?
If I survive, I will contrive,
To meet you all at pHusion.