2D-Deconvolution

[Chris Tully]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Andrew,

Have you looked at the Nikon Perfect Focus system or the Olympus ZDC?  These are both laser based systems that reflect an IR laser off the cover glass of your sample and maintain focus not based on image analysis but based on reading the reflected laser beam.  For the system you've described, I'd want to couple one of these with a software or hardware solution for finding the best focused plane based on image analysis and then trigger the laser system to maintain that position.

Chris Tully

On 8/28/07, Andrew Resnick <[hidden email]> wrote:

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As far as autofocus capabilities, there are some manufacturers that claim to have it- Nikon's setup for TIRF also comes to mind.  I've been on a personal mission at trade shows to (gently) berate the manufacturers to come up with a solution for focus drift due to thermal fluctuations- the hardware exists, the missing link is a decent software feedback loop.  None have expressed interest, the typical excuse being that thermal fluctuations have nothing to do with the optical performance of the microscope, and thus is not their problem.

Another capability I lobby for is the ability to acquire fast z-stacks- the camera should be the limiting rate.  Again, it's primarily a software issue and it's seen as a niche application.

As for pre-setting the alignment of the optics, my point wasn't that it is/was not possible, my point was that we didn't have the time to solve that particular issue in addition to the thousands of other issues.  Like any large project, what was needed was to recognize that not every problem could be solved, and to prioritize the issues. That wasn't done, so no problem got solved.

Andy

At 07:52 AM 8/26/2007, you wrote:

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This is really fascinating, and it's a crying shame that the project didn't get off the
ground.  It's also a classic example of how NASA is brilliant in spending huge sums
of money just to stuff things up.  (At the time of writing this I don't know whether the
latest Shuttle crew has safely returned to Earth or not, knowing that their heat shield
tiles have been holed by foam from the fuel tanks)
 
In terms of the design features, widefield autofocus has been available for years but
I can't vouch for the situation back in 1999.  I would have thought that for such a
tightly specified sample, Koehler illumination could have been preset, and likewise
I'd have thought that a suitably rugged phase contrast condenser would not require
re-aligning in orbit.   But 2 litres of immersion oil still worries me! 
 
Andrew, this is a most extraorinarily fascinating story, and I do hope that even
if the microscope didn't fly some useful land-based improvements to automated
microscopy flowed on from it.
 
                                                                                                                  Guy

---

From: Confocal Microscopy List on behalf of Robert J. Palmer Jr.
Sent: Sat 25/08/2007 4:54 AM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
This is all quite interesting from the standpoint of what NASA (and DOE and DOD) can dream up as tasks, and how they and the associated contractors approach them.  This particular example looks like a materials science track (?).  The thread originally dealt with a biological application.  I heard a talk from a person at Carnegie on his experience with designing an automated epifluorescence microscope intended for rover deployment.  This thing was used to photograph lichens in the Atacama desert.  There are no lichens (or fungi or algae) on the surface of Mars - MAYBE some fossilized bacteria or, if one is really really lucky, some bacterial spores (viability undetermined) near the poles.  So, the only way to hunt for these things is to do geological thin sections that can be examined using high resolution light microscopy (EM doesn't work, but Raman has!), then have an AI system (or real-time interpretation by a living scientist) to recognize things as bacteria - things that are not terribly different than abundant abiological geological "artifacts".
I would not be surprised to find out that a system like this has at least been proposed to NASA, if not gone to feasibility tests.  Anyway, that's the view from a professional pessimist......

PS - for those interested, a long-standing research route at NASA and ESA has been to look for bacteria in space (collection of particles and subsequent analysis/growth epxts.

Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Ok, here goes.  I apologize in advance for the length; it's just a sign of how committed I was to the project.

Let me first say that this project (the Light Microscopy Module, LMM) was an incredible experience for me, and I learned an amazing amount of stuff from some truly world-class engineers and technicians.  In my opinion, the failure of this project was due to the fear of NASA and contractor managers to make timely and unpopular decisions.  At it's peak, the LMM contractor team numbered about 50, there was another 10 NASA technical folks and the Principle Investigator (PI) teams added another 5 or 10 post-docs and grad students.

Here's some background: around 1998, NASA approved a group of experiments involving colloids and fluids for spaceflight on the International Space Station.  The first step in the process is for NASA to write a set of "requirements" for each experiment.  A "requirement" is some capability that the flight instrument must have in order to produce valid and useful scientific results.  For example, a requirement may be "obtain 30 images per second".  How these requirements come about is an interesting story in itself, but in the end, NASA provides a list of requirements as part of a contract bid- contractors look at the requirements list and come up with a proposal to build *something that meets the requirements* at a certain cost.  NASA then awards the contract to whomever it chooses.

I was hired by the contractor in late 1999, when a contract was being generated to fly a microscope. That is to say, the contractor management convinced NASA management that a microscope was *something that met the requirements* for 4 flight experiments.  Three of the experiments involved imaging and manipulating colloidal emulsions, while the fourth was a fluid heat transfer experiment, and the need was to image the wetting boundary.  There were approximately 300 pages (single spaced) of requirements.  At the time, none of us knew anything about microscopes specifically.

To summarize the early planning stage, what was needed was a completely automated, tricked-out microscope.  Not motorized, but *automated*.  Once we invented this particular instrument, quite a bit of excitement was generated throughout NASA, for obvious reasons.  It's cool, for one thing. Really sci-fi. The project rapidly blew up , attracting the NASA bio community as well.  Lots of color drawings were made and distributed around.  Websites were created.

At the time, we knew of no imaging system that will *automatically* focus on an unknown target within any sort of reasonable timeframe, and maintain focus as the sample is moved around.  We knew of no microscope system that will optimize (and automatically adjust) DIC shear for contrast.  We knew of no microscope system that will automatically align the phase rings in a phase contrast system.   We knew of no imaging system that would automatically establish Kohler illumination.  I still am not aware of any microscope that will do any of this. If I am wrong, I would certainly like to know about it.  When we did the project, we had to motorize the condenser turret and components, the epi- DIC prism, polarizer, and waveplate, the tube lens turret and Bertrand lens, the viewing prisms, all kinds of stuff.  And any existing motors that did not meet NASA specs had to be removed and replaced, the gears de-greased and re-greased with NASA approved grease, the chassis de-painted, bolts changed, wiring re-done, integrated circuits had to be replaced with radiation-hardened components.  I've disassembled and reassembled irises, stage slider bearings, and entire microscopes. Irises are the worst, by far.

We obtained from the manufacturer complete blueprints for the microscope and lenses.  Complete lens specifications and drawings.  Let me tell you- those high NA immersion apochromats are absolute marvels.

Here's how I would characterize the design phase: Imagine you work for GM, and GM wants a spiffy new car. You head the team that is in charge of the engine. LMM is the engine- the whole car is a larger structure that supplies the LMM with electricity, coolant, saves data, etc. etc.  So you are to design an engine to certain specifications- torque, horsepower, compression ratio, whatever. Problem: you don't know how much room you have in the hood.  You don't know where the transmission or exhaust will connect.  You don't know where the electrical connections are. You don't know anything except the engine requirements.  Your first step may be to decide on the piston arrangement- how many?  inline? V? rotary? In any case, off you go.  And as problems arise, you work to solve them. There will be meetings with the electrical team to decide where the alternator belt will go. Meetings with the fuel supply group to determine how much gas is needed.  This goes along reasonably well until someone claims that the car will not meet "car specifications"- maybe not enough miles per gallon. Who's fault is that- the transmission team or the engine team? Maybe it's the body design- too much drag or weight? Design teams now compete to show the other team is at fault. Money and time is wasted trying to meet unrealistic and arbitrary requirements.

Now we come to the safety concerns- astronauts are rare and delicate flowers, after all- touch temperatures (no convection to draw off heat) have to be below a certain value, the equipment must withstand "kick loads"- astronauts may kick off the microscope to propel themselves (!), anything breakable (including the samples and arc bulbs) has to be enclosed 3x.... chemicals, etc.  There were "leak paths" that had to be plugged- the objective turret head was re-designed, we thought about enclosing the immersion objectives with latex at some point, it's insane what has to be done in the name of 'safety'.  There was a 200+ page document with a list of safety concerns: for example, we calculated at most 2000 ml of immersion oil was required over the life of the 3 colloid experiments- so one question was "what happens if all 2000 ml is dispensed at once?"  Each concern required at least 3 pages of reply- a plan, a backup plan, a backup to the backup, and then a test, validation and verification procedure to ensure that one of the three plans would work.

Then the microscope is launched (up to 9 g's) in pieces and assembled on-orbit, without gravity loading things or keeping them in place.  This, after sitting in Florida in a non-environmentally controlled crate for several months.  And the space station is incredibly (mechanically) noisy.  And there are huge thermal swings, some from the microscope and light sources- and the fans we needed to move the heat off add to the vibrational environment.  This is why the microscope needed to be able to align the optical elements.

Remember, there is no user interface- it's all done by software.  We had no access to "diagnostic" images to determine if there is a problem.  There was no astronaut interface- no eyepiece, no computer screen to view what was being acquired. Again, imagine writing down instructions on how to set up a microscope from the box, giving the instructions to an undergraduate who has never done that before, and having the expectation that everything will work perfectly the first time (because you only get one chance to run the experiment- once the experiment is over, all you get is a stack of data tapes with all your images when the shuttle is able to bring them down).    In reality, it's even worse than that- you don't get to write the instructions, someone unfamiliar with how microscopes work writes down the instructions, occasionally asking for your input.

Confocal was (surprisingly) the easy one- we used a Yokogawa spinning disk- incredibly rugged, and the issue of "finding focus" is eliminated.  Confocal imaging would have met the overwhelming majority of imaging requirements for the colloid experiments.

Oil immersion is do-able, actually- the oil preferentially clings to the glass and objective, and we found some non-wetting coatings we could apply to control where the oil went.  The trick is dispensing the oil without bubbles.  We proved this out by flying a microscope on the KC-135 "vomit comet".  That was awesome.

And the data- we estimated 1 TB of information was going to be generated *per day* (the requirements were 30 frames/sec, 1k x 1k 12-bit images) for 12 months.  Where does the data go? Downlinking provided about 5 MB at best per day, IIRC.

Here's an example of what is right about NASA technical folks- one of the PIs wanted to fly about 1500 samples.   How on earth could we accommodate this? The solution was wafer-scale integration of sample cells- a glass disk 1 mm thick, just like a huge microscope slide, was bonded to a silicon wafer, which was then ground down to 100 microns thickness, so we could image the whole thickness.  The silicon was etched in the pattern we needed: rows and columns of holes shaped like '=0=', each hole/cell holding about 50 microliters of colloid. Each hole got a small magnetic stir bar, a fraction of a mm long, so each sample could be freshly mixed prior to imaging.  Then, a glass plate was bonded to the top and ground down to 150 microns thick: a # 1 1/2 coverslip. The silicon provided an excellent reflective surface- i.e. something to focus on, and we could pack in about 300 cells per sample tray.   We knew the exact position of everything, and the exact thickness of everything, so we solved quite a few problems in one fell swoop.  Of course, there is then the problem of filling and sealing 1500 50-microliter cells (each with different compositions- and the composition had to be verified somehow) that have to maintain their integrity for months, but we put that back onto the PI.

Anything that goes up in space is using 10-year old technology at best.  For gears and fans, that's not a big deal.  But it is for cameras. And data interlinks. And software.  Again, going back to the car analogy, once the piston layout is designed, a lot of things are constrained. And as the project moves along, it's harder and harder to change the piston layout.  Once a particular microscope was selected, we could not go back and even update to a newer model- we bought 5 sets of everything to ensure we had spare parts.

In the end, the NASA expectations (as sold to the PIs) were totally unrealistic, and the budget was likewise ridiculous.  NASA management honestly believed that we could simply buy what we needed, that there were no problems to be solved.  There was no money for testing and evaluation, among other things.  I really thought, until I left 5 years later, that we could deliver something that would meet about 80% of the requirements.  Unfortunately, management's only input was to periodically yell "failure is not an option!" and so we spent 80% of our time on the least important 20%.



At 10:42 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at  <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I agree, this is an excellent thread…
 
 
Alice Rodriguez, Ph.D.
Duke University
Rm 4331 French Family Science Center
Science Drive
Dept of Biology/DCMB Box 90338
Durham NC 27708
 
Mobile: [phone]
From: Confocal Microscopy List [ [hidden email]] On Behalf Of Evelyn Ralston
Sent: Friday, August 24, 2007 11:30 AM
To: [hidden email]
Subject: Re: A microscope on Mars?
 
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Please don't. It may not be what we think about every day but IMHO it's a very interesting thread.
 
Evelyn Ralston, Ph.D.
Head, Light imaging Section,
Office of Science and Technology, NIAMS, NIH
Rm 1535, Bldg 50
Bethesda MD 20892-8023
 
tel [phone]; FAX [phone]
 


 
On Aug 24, 2007, at 11:54 AM, Andrew Resnick wrote:


Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I don't want to bore everyone on this list,  so I'll take this offline.

Andy

At 08:50 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Well, automating oil immersion in zero gravity doesn't really
bear thinking about!  But automated microscopes (non-immersion)
in which you simply 'post' in a slide and look at the images on
a screen are available from several manufacturers - wouldn't
one of those have been a good starting point?  So far as I know
none are confocal but implementing confocal and spectrophotometry
would not be hard - laser tweezers might be more tricky.  DIC, phase
darkfield etc would be trivial.
 
                                                                            Guy

---

From: Confocal Microscopy List on behalf of Andrew Resnick
Sent: Fri 24/08/2007 11:29 PM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal My prior job was with a NASA contractor, our project was to put a full-featured microscope (brightfield, darkfield, phase contrast, DIC, confocal, laser tweezers, spectrophotometry, interferometry, oil immersion) onto the space station for (initially) 4 condensed-matter experiments, and later for biology.  Because of safety regulations, the microscope could not be operated by astronauts- they were to simply load a sample, close the door, and the machine would do its thing. You cannot imagine how difficult it is to automate a microscope- the oil immersion alone was a nightmare.  In the end, we were unable to pull it off.

There are some compact space-based microscopes (I think ESA has a phase contrast scope), but AFAIK, landers typically have chemical-based detectors as they are more sensitive and can be made more robust to the rigors of launch and landing.

At 09:03 PM 8/23/2007, you wrote:

Search the CONFOCAL archive at <a href="http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal A thought just occurred to me while reading a CNN news article about the planet Mars: Why not send an automated microscope with a robotic lander to look for life there in the soil? Surely more sophisticated instruments have been sent to Mars. Has NASA or any other space agency ever considered this kind of approach? Just curious.



John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging


Tel: W:416-946-5022
Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

 

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

-- 

Robert J. Palmer Jr., Ph.D.
Natl Inst Dental Craniofacial Res - Natl Insts Health
Oral Infection and Immunity Branch
Bldg 30, Room 310
30 Convent Drive
Bethesda MD 20892
ph 301-594-0025
fax [phone]

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

[George McNamara]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Ludl had a functional video autofocus circuit in their Z-motor board for the MAC2000 back in circa 1992. Jeff Price and many others have been publishing microscope autofocus routines for a decade+. NASA is brilliant in wasting huge sums of money.



At 10:56 AM 8/28/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal As far as autofocus capabilities, there are some manufacturers that claim to have it- Nikon's setup for TIRF also comes to mind.  I've been on a personal mission at trade shows to (gently) berate the manufacturers to come up with a solution for focus drift due to thermal fluctuations- the hardware exists, the missing link is a decent software feedback loop.  None have expressed interest, the typical excuse being that thermal fluctuations have nothing to do with the optical performance of the microscope, and thus is not their problem.

Another capability I lobby for is the ability to acquire fast z-stacks- the camera should be the limiting rate.  Again, it's primarily a software issue and it's seen as a niche application.

As for pre-setting the alignment of the optics, my point wasn't that it is/was not possible, my point was that we didn't have the time to solve that particular issue in addition to the thousands of other issues.  Like any large project, what was needed was to recognize that not every problem could be solved, and to prioritize the issues. That wasn't done, so no problem got solved.

Andy

At 07:52 AM 8/26/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
This is really fascinating, and it's a crying shame that the project didn't get off the
ground.  It's also a classic example of how NASA is brilliant in spending huge sums
of money just to stuff things up.  (At the time of writing this I don't know whether the
latest Shuttle crew has safely returned to Earth or not, knowing that their heat shield
tiles have been holed by foam from the fuel tanks)
 
In terms of the design features, widefield autofocus has been available for years but
I can't vouch for the situation back in 1999.  I would have thought that for such a
tightly specified sample, Koehler illumination could have been preset, and likewise
I'd have thought that a suitably rugged phase contrast condenser would not require
re-aligning in orbit.   But 2 litres of immersion oil still worries me! 
 
Andrew, this is a most extraorinarily fascinating story, and I do hope that even
if the microscope didn't fly some useful land-based improvements to automated
microscopy flowed on from it.
 
                                                                                                                  Guy

---

From: Confocal Microscopy List on behalf of Robert J. Palmer Jr.
Sent: Sat 25/08/2007 4:54 AM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
This is all quite interesting from the standpoint of what NASA (and DOE and DOD) can dream up as tasks, and how they and the associated contractors approach them.  This particular example looks like a materials science track (?).  The thread originally dealt with a biological application.  I heard a talk from a person at Carnegie on his experience with designing an automated epifluorescence microscope intended for rover deployment.  This thing was used to photograph lichens in the Atacama desert.  There are no lichens (or fungi or algae) on the surface of Mars - MAYBE some fossilized bacteria or, if one is really really lucky, some bacterial spores (viability undetermined) near the poles.  So, the only way to hunt for these things is to do geological thin sections that can be examined using high resolution light microscopy (EM doesn't work, but Raman has!), then have an AI system (or real-time interpretation by a living scientist) to recognize things as bacteria - things that are not terribly different than abundant abiological geological "artifacts".
I would not be surprised to find out that a system like this has at least been proposed to NASA, if not gone to feasibility tests.  Anyway, that's the view from a professional pessimist......

PS - for those interested, a long-standing research route at NASA and ESA has been to look for bacteria in space (collection of particles and subsequent analysis/growth epxts.

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Ok, here goes.  I apologize in advance for the length; it's just a sign of how committed I was to the project.

Let me first say that this project (the Light Microscopy Module, LMM) was an incredible experience for me, and I learned an amazing amount of stuff from some truly world-class engineers and technicians.  In my opinion, the failure of this project was due to the fear of NASA and contractor managers to make timely and unpopular decisions.  At it's peak, the LMM contractor team numbered about 50, there was another 10 NASA technical folks and the Principle Investigator (PI) teams added another 5 or 10 post-docs and grad students.

Here's some background: around 1998, NASA approved a group of experiments involving colloids and fluids for spaceflight on the International Space Station.  The first step in the process is for NASA to write a set of "requirements" for each experiment.  A "requirement" is some capability that the flight instrument must have in order to produce valid and useful scientific results.  For example, a requirement may be "obtain 30 images per second".  How these requirements come about is an interesting story in itself, but in the end, NASA provides a list of requirements as part of a contract bid- contractors look at the requirements list and come up with a proposal to build *something that meets the requirements* at a certain cost.  NASA then awards the contract to whomever it chooses.

I was hired by the contractor in late 1999, when a contract was being generated to fly a microscope. That is to say, the contractor management convinced NASA management that a microscope was *something that met the requirements* for 4 flight experiments.  Three of the experiments involved imaging and manipulating colloidal emulsions, while the fourth was a fluid heat transfer experiment, and the need was to image the wetting boundary.  There were approximately 300 pages (single spaced) of requirements.  At the time, none of us knew anything about microscopes specifically.

To summarize the early planning stage, what was needed was a completely automated, tricked-out microscope.  Not motorized, but *automated*.  Once we invented this particular instrument, quite a bit of excitement was generated throughout NASA, for obvious reasons.  It's cool, for one thing. Really sci-fi. The project rapidly blew up , attracting the NASA bio community as well.  Lots of color drawings were made and distributed around.  Websites were created.

At the time, we knew of no imaging system that will *automatically* focus on an unknown target within any sort of reasonable timeframe, and maintain focus as the sample is moved around.  We knew of no microscope system that will optimize (and automatically adjust) DIC shear for contrast.  We knew of no microscope system that will automatically align the phase rings in a phase contrast system.   We knew of no imaging system that would automatically establish Kohler illumination.  I still am not aware of any microscope that will do any of this. If I am wrong, I would certainly like to know about it.  When we did the project, we had to motorize the condenser turret and components, the epi- DIC prism, polarizer, and waveplate, the tube lens turret and Bertrand lens, the viewing prisms, all kinds of stuff.  And any existing motors that did not meet NASA specs had to be removed and replaced, the gears de-greased and re-greased with NASA approved grease, the chassis de-painted, bolts changed, wiring re-done, integrated circuits had to be replaced with radiation-hardened components.  I've disassembled and reassembled irises, stage slider bearings, and entire microscopes. Irises are the worst, by far.

We obtained from the manufacturer complete blueprints for the microscope and lenses.  Complete lens specifications and drawings.  Let me tell you- those high NA immersion apochromats are absolute marvels.

Here's how I would characterize the design phase: Imagine you work for GM, and GM wants a spiffy new car. You head the team that is in charge of the engine. LMM is the engine- the whole car is a larger structure that supplies the LMM with electricity, coolant, saves data, etc. etc.  So you are to design an engine to certain specifications- torque, horsepower, compression ratio, whatever. Problem: you don't know how much room you have in the hood.  You don't know where the transmission or exhaust will connect.  You don't know where the electrical connections are. You don't know anything except the engine requirements.  Your first step may be to decide on the piston arrangement- how many?  inline? V? rotary? In any case, off you go.  And as problems arise, you work to solve them. There will be meetings with the electrical team to decide where the alternator belt will go. Meetings with the fuel supply group to determine how much gas is needed.  This goes along reasonably well until someone claims that the car will not meet "car specifications"- maybe not enough miles per gallon. Who's fault is that- the transmission team or the engine team? Maybe it's the body design- too much drag or weight? Design teams now compete to show the other team is at fault. Money and time is wasted trying to meet unrealistic and arbitrary requirements.

Now we come to the safety concerns- astronauts are rare and delicate flowers, after all- touch temperatures (no convection to draw off heat) have to be below a certain value, the equipment must withstand "kick loads"- astronauts may kick off the microscope to propel themselves (!), anything breakable (including the samples and arc bulbs) has to be enclosed 3x.... chemicals, etc.  There were "leak paths" that had to be plugged- the objective turret head was re-designed, we thought about enclosing the immersion objectives with latex at some point, it's insane what has to be done in the name of 'safety'.  There was a 200+ page document with a list of safety concerns: for example, we calculated at most 2000 ml of immersion oil was required over the life of the 3 colloid experiments- so one question was "what happens if all 2000 ml is dispensed at once?"  Each concern required at least 3 pages of reply- a plan, a backup plan, a backup to the backup, and then a test, validation and verification procedure to ensure that one of the three plans would work.

Then the microscope is launched (up to 9 g's) in pieces and assembled on-orbit, without gravity loading things or keeping them in place.  This, after sitting in Florida in a non-environmentally controlled crate for several months.  And the space station is incredibly (mechanically) noisy.  And there are huge thermal swings, some from the microscope and light sources- and the fans we needed to move the heat off add to the vibrational environment.  This is why the microscope needed to be able to align the optical elements.

Remember, there is no user interface- it's all done by software.  We had no access to "diagnostic" images to determine if there is a problem.  There was no astronaut interface- no eyepiece, no computer screen to view what was being acquired. Again, imagine writing down instructions on how to set up a microscope from the box, giving the instructions to an undergraduate who has never done that before, and having the expectation that everything will work perfectly the first time (because you only get one chance to run the experiment- once the experiment is over, all you get is a stack of data tapes with all your images when the shuttle is able to bring them down).    In reality, it's even worse than that- you don't get to write the instructions, someone unfamiliar with how microscopes work writes down the instructions, occasionally asking for your input.

Confocal was (surprisingly) the easy one- we used a Yokogawa spinning disk- incredibly rugged, and the issue of "finding focus" is eliminated.  Confocal imaging would have met the overwhelming majority of imaging requirements for the colloid experiments.

Oil immersion is do-able, actually- the oil preferentially clings to the glass and objective, and we found some non-wetting coatings we could apply to control where the oil went.  The trick is dispensing the oil without bubbles.  We proved this out by flying a microscope on the KC-135 "vomit comet".  That was awesome.

And the data- we estimated 1 TB of information was going to be generated *per day* (the requirements were 30 frames/sec, 1k x 1k 12-bit images) for 12 months.  Where does the data go? Downlinking provided about 5 MB at best per day, IIRC.

Here's an example of what is right about NASA technical folks- one of the PIs wanted to fly about 1500 samples.   How on earth could we accommodate this? The solution was wafer-scale integration of sample cells- a glass disk 1 mm thick, just like a huge microscope slide, was bonded to a silicon wafer, which was then ground down to 100 microns thickness, so we could image the whole thickness.  The silicon was etched in the pattern we needed: rows and columns of holes shaped like '=0=', each hole/cell holding about 50 microliters of colloid. Each hole got a small magnetic stir bar, a fraction of a mm long, so each sample could be freshly mixed prior to imaging.  Then, a glass plate was bonded to the top and ground down to 150 microns thick: a # 1 1/2 coverslip. The silicon provided an excellent reflective surface- i.e. something to focus on, and we could pack in about 300 cells per sample tray.   We knew the exact position of everything, and the exact thickness of everything, so we solved quite a few problems in one fell swoop.  Of course, there is then the problem of filling and sealing 1500 50-microliter cells (each with different compositions- and the composition had to be verified somehow) that have to maintain their integrity for months, but we put that back onto the PI.

Anything that goes up in space is using 10-year old technology at best.  For gears and fans, that's not a big deal.  But it is for cameras. And data interlinks. And software.  Again, going back to the car analogy, once the piston layout is designed, a lot of things are constrained. And as the project moves along, it's harder and harder to change the piston layout.  Once a particular microscope was selected, we could not go back and even update to a newer model- we bought 5 sets of everything to ensure we had spare parts.

In the end, the NASA expectations (as sold to the PIs) were totally unrealistic, and the budget was likewise ridiculous.  NASA management honestly believed that we could simply buy what we needed, that there were no problems to be solved.  There was no money for testing and evaluation, among other things.  I really thought, until I left 5 years later, that we could deliver something that would meet about 80% of the requirements.  Unfortunately, management's only input was to periodically yell "failure is not an option!" and so we spent 80% of our time on the least important 20%.



At 10:42 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at  http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I agree, this is an excellent thread…
 
 
Alice Rodriguez, Ph.D.
Duke University
Rm 4331 French Family Science Center
Science Drive
Dept of Biology/DCMB Box 90338
Durham NC 27708
 
Mobile: [phone]
From: Confocal Microscopy List [ [hidden email]] On Behalf Of Evelyn Ralston
Sent: Friday, August 24, 2007 11:30 AM
To: [hidden email]
Subject: Re: A microscope on Mars?
 
Search the CONFOCAL archive at  http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Please don't. It may not be what we think about every day but IMHO it's a very interesting thread.
 
Evelyn Ralston, Ph.D.
Head, Light imaging Section,
Office of Science and Technology, NIAMS, NIH
Rm 1535, Bldg 50
Bethesda MD 20892-8023
 
tel [phone]; FAX [phone]
 


 
On Aug 24, 2007, at 11:54 AM, Andrew Resnick wrote:


Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I don't want to bore everyone on this list,  so I'll take this offline.

Andy

At 08:50 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Well, automating oil immersion in zero gravity doesn't really
bear thinking about!  But automated microscopes (non-immersion)
in which you simply 'post' in a slide and look at the images on
a screen are available from several manufacturers - wouldn't
one of those have been a good starting point?  So far as I know
none are confocal but implementing confocal and spectrophotometry
would not be hard - laser tweezers might be more tricky.  DIC, phase
darkfield etc would be trivial.
 
                                                                            Guy

---

From: Confocal Microscopy List on behalf of Andrew Resnick
Sent: Fri 24/08/2007 11:29 PM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal My prior job was with a NASA contractor, our project was to put a full-featured microscope (brightfield, darkfield, phase contrast, DIC, confocal, laser tweezers, spectrophotometry, interferometry, oil immersion) onto the space station for (initially) 4 condensed-matter experiments, and later for biology.  Because of safety regulations, the microscope could not be operated by astronauts- they were to simply load a sample, close the door, and the machine would do its thing. You cannot imagine how difficult it is to automate a microscope- the oil immersion alone was a nightmare.  In the end, we were unable to pull it off.

There are some compact space-based microscopes (I think ESA has a phase contrast scope), but AFAIK, landers typically have chemical-based detectors as they are more sensitive and can be made more robust to the rigors of launch and landing.

At 09:03 PM 8/23/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal A thought just occurred to me while reading a CNN news article about the planet Mars: Why not send an automated microscope with a robotic lander to look for life there in the soil? Surely more sophisticated instruments have been sent to Mars. Has NASA or any other space agency ever considered this kind of approach? Just curious.



John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging


Tel: W:416-946-5022
Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

 

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

-- 

Robert J. Palmer Jr., Ph.D.
Natl Inst Dental Craniofacial Res - Natl Insts Health
Oral Infection and Immunity Branch
Bldg 30, Room 310
30 Convent Drive
Bethesda MD 20892
ph 301-594-0025
fax [phone]

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

 

George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office

[Peter Drain]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I second Andrew's lobby for imaging acquisition software vendors to acquire z-stacks at rates that make the camera rate limiting.

This should be a standard for the popular 512 x 512 EM-CCD cameras and those software packages designed to run these cameras, yet is surprisingly commonly lacking. Once the overhead problems are resolved by all vendors (some vendors already have in fact), the data throughput to hard drives should be made more durable. It seems the latter will be well-accommodated once 64 bit technology becomes more common. This area of confocal microscopy is fundamental to its applications in live-cell biology (not a niche application at least here at all) and such acquisition rates are not only needed now but will need to increment with the technical capability improvements in the cameras and with the complexity of the scientific problems being studied over the years. 

Peter Drain, PhD

Department of Cell Biology and Physiology

Room 323, Biomedical Science Tower South

3500 Terrace Street

Pittsburgh, PA   15261

Phone: [phone]

Email:              [hidden email]

URL:        www.cbp.pitt.edu/faculty/drain.html

On Aug 28, 2007, at 10:56 AM, Andrew Resnick wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal As far as autofocus capabilities, there are some manufacturers that claim to have it- Nikon's setup for TIRF also comes to mind.  I've been on a personal mission at trade shows to (gently) berate the manufacturers to come up with a solution for focus drift due to thermal fluctuations- the hardware exists, the missing link is a decent software feedback loop.  None have expressed interest, the typical excuse being that thermal fluctuations have nothing to do with the optical performance of the microscope, and thus is not their problem.

Another capability I lobby for is the ability to acquire fast z-stacks- the camera should be the limiting rate.  Again, it's primarily a software issue and it's seen as a niche application.

As for pre-setting the alignment of the optics, my point wasn't that it is/was not possible, my point was that we didn't have the time to solve that particular issue in addition to the thousands of other issues.  Like any large project, what was needed was to recognize that not every problem could be solved, and to prioritize the issues. That wasn't done, so no problem got solved.

Andy

At 07:52 AM 8/26/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
This is really fascinating, and it's a crying shame that the project didn't get off the
ground.  It's also a classic example of how NASA is brilliant in spending huge sums
of money just to stuff things up.  (At the time of writing this I don't know whether the
latest Shuttle crew has safely returned to Earth or not, knowing that their heat shield
tiles have been holed by foam from the fuel tanks)
 
In terms of the design features, widefield autofocus has been available for years but
I can't vouch for the situation back in 1999.  I would have thought that for such a
tightly specified sample, Koehler illumination could have been preset, and likewise
I'd have thought that a suitably rugged phase contrast condenser would not require
re-aligning in orbit.   But 2 litres of immersion oil still worries me! 
 
Andrew, this is a most extraorinarily fascinating story, and I do hope that even
if the microscope didn't fly some useful land-based improvements to automated
microscopy flowed on from it.
 
                                                                                                                  Guy

---

From: Confocal Microscopy List on behalf of Robert J. Palmer Jr.
Sent: Sat 25/08/2007 4:54 AM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
This is all quite interesting from the standpoint of what NASA (and DOE and DOD) can dream up as tasks, and how they and the associated contractors approach them.  This particular example looks like a materials science track (?).  The thread originally dealt with a biological application.  I heard a talk from a person at Carnegie on his experience with designing an automated epifluorescence microscope intended for rover deployment.  This thing was used to photograph lichens in the Atacama desert.  There are no lichens (or fungi or algae) on the surface of Mars - MAYBE some fossilized bacteria or, if one is really really lucky, some bacterial spores (viability undetermined) near the poles.  So, the only way to hunt for these things is to do geological thin sections that can be examined using high resolution light microscopy (EM doesn't work, but Raman has!), then have an AI system (or real-time interpretation by a living scientist) to recognize things as bacteria - things that are not terribly different than abundant abiological geological "artifacts".
I would not be surprised to find out that a system like this has at least been proposed to NASA, if not gone to feasibility tests.  Anyway, that's the view from a professional pessimist......

PS - for those interested, a long-standing research route at NASA and ESA has been to look for bacteria in space (collection of particles and subsequent analysis/growth epxts.

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Ok, here goes.  I apologize in advance for the length; it's just a sign of how committed I was to the project.

Let me first say that this project (the Light Microscopy Module, LMM) was an incredible experience for me, and I learned an amazing amount of stuff from some truly world-class engineers and technicians.  In my opinion, the failure of this project was due to the fear of NASA and contractor managers to make timely and unpopular decisions.  At it's peak, the LMM contractor team numbered about 50, there was another 10 NASA technical folks and the Principle Investigator (PI) teams added another 5 or 10 post-docs and grad students.

Here's some background: around 1998, NASA approved a group of experiments involving colloids and fluids for spaceflight on the International Space Station.  The first step in the process is for NASA to write a set of "requirements" for each experiment.  A "requirement" is some capability that the flight instrument must have in order to produce valid and useful scientific results.  For example, a requirement may be "obtain 30 images per second".  How these requirements come about is an interesting story in itself, but in the end, NASA provides a list of requirements as part of a contract bid- contractors look at the requirements list and come up with a proposal to build *something that meets the requirements* at a certain cost.  NASA then awards the contract to whomever it chooses.

I was hired by the contractor in late 1999, when a contract was being generated to fly a microscope. That is to say, the contractor management convinced NASA management that a microscope was *something that met the requirements* for 4 flight experiments.  Three of the experiments involved imaging and manipulating colloidal emulsions, while the fourth was a fluid heat transfer experiment, and the need was to image the wetting boundary.  There were approximately 300 pages (single spaced) of requirements.  At the time, none of us knew anything about microscopes specifically.

To summarize the early planning stage, what was needed was a completely automated, tricked-out microscope.  Not motorized, but *automated*.  Once we invented this particular instrument, quite a bit of excitement was generated throughout NASA, for obvious reasons.  It's cool, for one thing. Really sci-fi. The project rapidly blew up , attracting the NASA bio community as well.  Lots of color drawings were made and distributed around.  Websites were created.

At the time, we knew of no imaging system that will *automatically* focus on an unknown target within any sort of reasonable timeframe, and maintain focus as the sample is moved around.  We knew of no microscope system that will optimize (and automatically adjust) DIC shear for contrast.  We knew of no microscope system that will automatically align the phase rings in a phase contrast system.   We knew of no imaging system that would automatically establish Kohler illumination.  I still am not aware of any microscope that will do any of this. If I am wrong, I would certainly like to know about it.  When we did the project, we had to motorize the condenser turret and components, the epi- DIC prism, polarizer, and waveplate, the tube lens turret and Bertrand lens, the viewing prisms, all kinds of stuff.  And any existing motors that did not meet NASA specs had to be removed and replaced, the gears de-greased and re-greased with NASA approved grease, the chassis de-painted, bolts changed, wiring re-done, integrated circuits had to be replaced with radiation-hardened components.  I've disassembled and reassembled irises, stage slider bearings, and entire microscopes. Irises are the worst, by far.

We obtained from the manufacturer complete blueprints for the microscope and lenses.  Complete lens specifications and drawings.  Let me tell you- those high NA immersion apochromats are absolute marvels.

Here's how I would characterize the design phase: Imagine you work for GM, and GM wants a spiffy new car. You head the team that is in charge of the engine. LMM is the engine- the whole car is a larger structure that supplies the LMM with electricity, coolant, saves data, etc. etc.  So you are to design an engine to certain specifications- torque, horsepower, compression ratio, whatever. Problem: you don't know how much room you have in the hood.  You don't know where the transmission or exhaust will connect.  You don't know where the electrical connections are. You don't know anything except the engine requirements.  Your first step may be to decide on the piston arrangement- how many?  inline? V? rotary? In any case, off you go.  And as problems arise, you work to solve them. There will be meetings with the electrical team to decide where the alternator belt will go. Meetings with the fuel supply group to determine how much gas is needed.  This goes along reasonably well until someone claims that the car will not meet "car specifications"- maybe not enough miles per gallon. Who's fault is that- the transmission team or the engine team? Maybe it's the body design- too much drag or weight? Design teams now compete to show the other team is at fault. Money and time is wasted trying to meet unrealistic and arbitrary requirements.

Now we come to the safety concerns- astronauts are rare and delicate flowers, after all- touch temperatures (no convection to draw off heat) have to be below a certain value, the equipment must withstand "kick loads"- astronauts may kick off the microscope to propel themselves (!), anything breakable (including the samples and arc bulbs) has to be enclosed 3x.... chemicals, etc.  There were "leak paths" that had to be plugged- the objective turret head was re-designed, we thought about enclosing the immersion objectives with latex at some point, it's insane what has to be done in the name of 'safety'.  There was a 200+ page document with a list of safety concerns: for example, we calculated at most 2000 ml of immersion oil was required over the life of the 3 colloid experiments- so one question was "what happens if all 2000 ml is dispensed at once?"  Each concern required at least 3 pages of reply- a plan, a backup plan, a backup to the backup, and then a test, validation and verification procedure to ensure that one of the three plans would work.

Then the microscope is launched (up to 9 g's) in pieces and assembled on-orbit, without gravity loading things or keeping them in place.  This, after sitting in Florida in a non-environmentally controlled crate for several months.  And the space station is incredibly (mechanically) noisy.  And there are huge thermal swings, some from the microscope and light sources- and the fans we needed to move the heat off add to the vibrational environment.  This is why the microscope needed to be able to align the optical elements.

Remember, there is no user interface- it's all done by software.  We had no access to "diagnostic" images to determine if there is a problem.  There was no astronaut interface- no eyepiece, no computer screen to view what was being acquired. Again, imagine writing down instructions on how to set up a microscope from the box, giving the instructions to an undergraduate who has never done that before, and having the expectation that everything will work perfectly the first time (because you only get one chance to run the experiment- once the experiment is over, all you get is a stack of data tapes with all your images when the shuttle is able to bring them down).    In reality, it's even worse than that- you don't get to write the instructions, someone unfamiliar with how microscopes work writes down the instructions, occasionally asking for your input.

Confocal was (surprisingly) the easy one- we used a Yokogawa spinning disk- incredibly rugged, and the issue of "finding focus" is eliminated.  Confocal imaging would have met the overwhelming majority of imaging requirements for the colloid experiments.

Oil immersion is do-able, actually- the oil preferentially clings to the glass and objective, and we found some non-wetting coatings we could apply to control where the oil went.  The trick is dispensing the oil without bubbles.  We proved this out by flying a microscope on the KC-135 "vomit comet".  That was awesome.

And the data- we estimated 1 TB of information was going to be generated *per day* (the requirements were 30 frames/sec, 1k x 1k 12-bit images) for 12 months.  Where does the data go? Downlinking provided about 5 MB at best per day, IIRC.

Here's an example of what is right about NASA technical folks- one of the PIs wanted to fly about 1500 samples.   How on earth could we accommodate this? The solution was wafer-scale integration of sample cells- a glass disk 1 mm thick, just like a huge microscope slide, was bonded to a silicon wafer, which was then ground down to 100 microns thickness, so we could image the whole thickness.  The silicon was etched in the pattern we needed: rows and columns of holes shaped like '=0=', each hole/cell holding about 50 microliters of colloid. Each hole got a small magnetic stir bar, a fraction of a mm long, so each sample could be freshly mixed prior to imaging.  Then, a glass plate was bonded to the top and ground down to 150 microns thick: a # 1 1/2 coverslip. The silicon provided an excellent reflective surface- i.e. something to focus on, and we could pack in about 300 cells per sample tray.   We knew the exact position of everything, and the exact thickness of everything, so we solved quite a few problems in one fell swoop.  Of course, there is then the problem of filling and sealing 1500 50-microliter cells (each with different compositions- and the composition had to be verified somehow) that have to maintain their integrity for months, but we put that back onto the PI.

Anything that goes up in space is using 10-year old technology at best.  For gears and fans, that's not a big deal.  But it is for cameras. And data interlinks. And software.  Again, going back to the car analogy, once the piston layout is designed, a lot of things are constrained. And as the project moves along, it's harder and harder to change the piston layout.  Once a particular microscope was selected, we could not go back and even update to a newer model- we bought 5 sets of everything to ensure we had spare parts.

In the end, the NASA expectations (as sold to the PIs) were totally unrealistic, and the budget was likewise ridiculous.  NASA management honestly believed that we could simply buy what we needed, that there were no problems to be solved.  There was no money for testing and evaluation, among other things.  I really thought, until I left 5 years later, that we could deliver something that would meet about 80% of the requirements.  Unfortunately, management's only input was to periodically yell "failure is not an option!" and so we spent 80% of our time on the least important 20%.



At 10:42 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at  http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
I agree, this is an excellent thread…
 
 
Alice Rodriguez, Ph.D.
Duke University
Rm 4331 French Family Science Center
Science Drive
Dept of Biology/DCMB Box 90338
Durham NC 27708
 
Mobile: [phone]
From: Confocal Microscopy List [ [hidden email]] On Behalf Of Evelyn Ralston
Sent: Friday, August 24, 2007 11:30 AM
To: [hidden email]
Subject: Re: A microscope on Mars?
 
Search the CONFOCAL archive at  http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Please don't. It may not be what we think about every day but IMHO it's a very interesting thread.
 
Evelyn Ralston, Ph.D.
Head, Light imaging Section,
Office of Science and Technology, NIAMS, NIH
Rm 1535, Bldg 50
Bethesda MD 20892-8023
 
tel [phone]; FAX [phone]
 


 
On Aug 24, 2007, at 11:54 AM, Andrew Resnick wrote:


Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I don't want to bore everyone on this list,  so I'll take this offline.

Andy

At 08:50 AM 8/24/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
Well, automating oil immersion in zero gravity doesn't really
bear thinking about!  But automated microscopes (non-immersion)
in which you simply 'post' in a slide and look at the images on
a screen are available from several manufacturers - wouldn't
one of those have been a good starting point?  So far as I know
none are confocal but implementing confocal and spectrophotometry
would not be hard - laser tweezers might be more tricky.  DIC, phase
darkfield etc would be trivial.
 
                                                                            Guy

---

From: Confocal Microscopy List on behalf of Andrew Resnick
Sent: Fri 24/08/2007 11:29 PM
To: [hidden email]
Subject: Re: A microscope on Mars?

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal My prior job was with a NASA contractor, our project was to put a full-featured microscope (brightfield, darkfield, phase contrast, DIC, confocal, laser tweezers, spectrophotometry, interferometry, oil immersion) onto the space station for (initially) 4 condensed-matter experiments, and later for biology.  Because of safety regulations, the microscope could not be operated by astronauts- they were to simply load a sample, close the door, and the machine would do its thing. You cannot imagine how difficult it is to automate a microscope- the oil immersion alone was a nightmare.  In the end, we were unable to pull it off.

There are some compact space-based microscopes (I think ESA has a phase contrast scope), but AFAIK, landers typically have chemical-based detectors as they are more sensitive and can be made more robust to the rigors of launch and landing.

At 09:03 PM 8/23/2007, you wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal A thought just occurred to me while reading a CNN news article about the planet Mars: Why not send an automated microscope with a robotic lander to look for life there in the soil? Surely more sophisticated instruments have been sent to Mars. Has NASA or any other space agency ever considered this kind of approach? Just curious.



John Oreopoulos, BSc,

PhD Candidate

University of Toronto

Institute For Biomaterials and Biomedical Engineering

Centre For Studies in Molecular Imaging


Tel: W:416-946-5022
Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

 

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

-- 

Robert J. Palmer Jr., Ph.D.
Natl Inst Dental Craniofacial Res - Natl Insts Health
Oral Infection and Immunity Branch
Bldg 30, Room 310
30 Convent Drive
Bethesda MD 20892
ph 301-594-0025
fax [phone]

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)

[Andrew Resnick]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I debated responding to this, but the last sentence is too tempting-
I'll take the bait.

Since the majority of people on this list receive government funding
either for their instrumentation, salary, or both, I think we should
all be a lot more careful in claiming that other science agencies are
wasteful (or more wasteful) in expenditures.  All NASA funded
projects are peer reviewed, and all large projects are "brilliant in
wasting huge sums of money".

As for the specific suggestion, let me put it like this: I am putting
together a puzzle, and a single piece is missing.  What costs less:

1) custom making my own piece
2) accepting some random ill-fitting piece, and re-cutting the entire
puzzle to accept the proffered item?

Andy


At 06:16 PM 8/28/2007, you wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>Ludl had a functional video autofocus circuit in their Z-motor board
>for the MAC2000 back in circa 1992. Jeff Price and many others have
>been publishing microscope autofocus routines for a decade+. NASA is
>brilliant in wasting huge sums of money.
>
>
>
>At 10:56 AM 8/28/2007, you wrote:
>>Search the CONFOCAL archive at
>>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal As far as
>>autofocus capabilities, there are some manufacturers that claim to
>>have it- Nikon's setup for TIRF also comes to mind.  I've been on a
>>personal mission at trade shows to (gently) berate the
>>manufacturers to come up with a solution for focus drift due to
>>thermal fluctuations- the hardware exists, the missing link is a
>>decent software feedback loop.  None have expressed interest, the
>>typical excuse being that thermal fluctuations have nothing to do
>>with the optical performance of the microscope, and thus is not their problem.
>>
>>Another capability I lobby for is the ability to acquire fast
>>z-stacks- the camera should be the limiting rate.  Again, it's
>>primarily a software issue and it's seen as a niche application.
>>
>>As for pre-setting the alignment of the optics, my point wasn't
>>that it is/was not possible, my point was that we didn't have the
>>time to solve that particular issue in addition to the thousands of
>>other issues.  Like any large project, what was needed was to
>>recognize that not every problem could be solved, and to prioritize
>>the issues. That wasn't done, so no problem got solved.
>>
>>Andy

Andrew Resnick, Ph. D.
Instructor
Department of Physiology and Biophysics
Case Western Reserve University
216-368-6899 (V)
216-368-4223 (F)