Tuesday, February 21, 2012

Laboratory Microscope Upgrade

We have an old Olympus IX-70 fluorescent microscope in our lab at Mizzou that has been here for at least a decade.  Although it's a very nice scope, it's been pretty badly neglected over the past few years and has fallen a bit into disrepair.  For my fluorescent microscopy needs, I've been using another professor's brand new microscope with good results.  But recently, an undergraduate researcher in our lab expressed a need to take data using a fluorescent microscope.  Unfortunately, the fluorescent microscope that I've been using is housed in a user facility, and the student would need training and special permission - not to mention pay an exorbitant fee - to access the facility.  So I decided this might be a good opportunity to upgrade our IX-70 and get it back into good working order.

The first step was to order a new dust cover and eyepieces.  At around the same time these items arrived, we had a certified technician come over from St. Louis to adjust and align the optics so that everything would be nicely dialed in.  This particular microscope has a trinocular design, which means that it has three different light paths for viewing a specimen.  With the first setting, the eyepieces are used to view the specimen.  With the second, the image is sent into the side port, which is equipped with a digital camera.  When the third setting is used, the light path is split, with 20% of the signal going to the eyepieces and the other 80% going to the front port.  As you can see in the picture below, the front port is connected to a 35mm camera.  Since we have no need for a 35mm camera, particularly with a digital camera on the side port, I thought it would be nice to equip the front port with a more useful piece of hardware.  And for our applications, it doesn't get much more useful than a spectrometer.

We had an extra Ocean Optics USB4000 handheld spectrometer that no one was using, but I needed a way to interface it with the microscope.  So first, I ordered an adapter from ThorLabs with 1" female threading that would attach to the microscope's front port.  When we received the adapter, I was disappointed to find that it was slightly too small for the front port, so that when the set screws were tightened the adapter was pushed to one side and no longer centered.  The shop guys in our department machined a beautiful collar for the adapter, which allows the adapter to slide snugly into place, but includes holes that allow the set screws to be tightened effectively.  Next, I threaded an SMA adapter into the 1" threading in the center of the adapter; this adapter is what the optical fiber will screw on to.  I also built and attached a lens tube to the backside of the adapter.  The lens tube slides into the microscope housing and directs the light from the specimen right onto the center of the SMA adapter and into the optical fiber.  With the adapter in place, the front port now looks more like this:

And here it is with the spectrometer connected to it:

Earlier this week, we put in another order for a brightfield filter that will give a more natural white light to our brightfield images.  Also included in the order was a new mercury bulb for the fluorescence lamp.  When these items have been installed, our old IX-70 will literally be better than brand new.  And there's been talk of ordering a new camera for the scope sometime this summer, which would also be a big upgrade.

Wednesday, February 15, 2012

Not The Worst News Ever

The president has released his proposed 2013 federal budget and ScienceInsider has been rolling out updates on how the budget is set to affect science funding.  You can find a list of recent posts related to the budget here.  Also, Wired Science has weighed in with a post on proposed cuts in the NASA budget.

Since I'm not an expert in such matters, and since the subject has obviously been tackled by folks who are much more knowledgeable than yours truly, I'd rather not delve into the details of the president's proposed budget.  I will, however, sum up the whole situation as I understand it by saying that the field of science is receiving a mixed bag by the administration's budget.  A lot of department budgets are being cut, but money is then being shuffled around so that science and research funding in these departments will actually be increased relative to the previous year.  Except for NASA.  Their funding is being cut and programs are being cancelled, so it seems to be all bad news for the space agency.

So I guess all-in-all, its only slightly bad news.  Not horrific.  But not good, either.

Tuesday, February 7, 2012

Your New Wallpaper

Most of you have probably already come across these new images of Earth taken by the Suomi National Polar-Orbiting Partnership.  The images are being called the new 'Blue Marble' after the original 'Blue Marble' image that was taken by the crew of Apollo 17 on their way to the moon.  The new 2012 Blue Marble is just ridiculously spectacular.  The images found on the NASA website are big-time high resolution and are definitely worth checking out.  And unless you're vehemently opposed to any desktop wallpaper other than Lolcats or something like that, I recommend saving the image (either hemisphere) as your background.  It's certainly a dazzling reminder of our both our insignificance and our accountability.

And if you're interested, Wired Science has a pretty good article on how the new Blue Marble images were taken and constructed.

Sunday, January 29, 2012

Bad Winter

I know some of you will wholeheartedly disagree with me on this one, but the winter so far this year has sucked!  If memory serves, we've gotten roughly two-and-a-half inches of snow so far this winter and we've only had a handful of below-freezing days.  And all this with department stores starting to roll out their spring clothing lines.  I suffered through the hot, hot heat of summer with the expectation that I would feel sweet relief in the form of cold, snowy days on which to drink big, scary beers and make pots of soup.  And an unseasonably warm, dry winter has ruined everything.  It's a goddam travesty is what it is.

As it turns out, there are a couple of meteorological phenomena that have compounded to produce the horrific winter that we're currently experiencing.  I ran across a good article describing the reasons for our crappy winter at Discovery News, via Pharyngula.  The first reason is La Nina, which has pushed the jet stream north - interestingly, La Nina was partially responsible for last year's harsh winter weather - and La Nina has combined with Arctic Oscillation and North Atlantic Oscillation, which have matched their phases, pulling the few weather systems that form over North America out into the Atlantic. I don't claim to be well versed in meteorology, so I won't even attempt any sort of in-depth discussion of this process.  But according to the article, we may return to some semblance of a real winter later this month.  I suppose time will tell.

All I know is that this has been a really lame winter so far.

Tuesday, January 24, 2012

Social Media and Scientific Journals

There have been rumblings of major changes in the way scientific journals peer review submissions.  Criticism of the current system has been growing for quite some time, particularly with respect to the lag time between when a manuscript is submitted and when it is published.  In the fast-paced world of modern research, by the time a paper is published - which can be many months after submission - it is often already out-of-date.  Some publishers have also faced criticism of favoritism, with lower quality papers being chosen over higher quality papers solely due to the name or affiliation of the author(s).

The first step towards a major paradigm shift in peer review has already occurred:  a social media network has been created by a group in Finland that is dedicated to reviewing manuscripts for publication in a Wiley journal.  Science Insider has a pretty good description of how the network functions and why it will be better than the current system, so I won't dwell on it.  But I will say that I'm still on the fence about this.  I think it's good that they're doing some cautious beta testing on one scientific journal, rather than instituting it widely right out of the gate, as it will allow Wiley to gather some valuable data, test the waters, and optimize the network before moving forward.  I'll definitely be keeping a close watch on this, because it represents a substantial change in the way peer reviewed journals select papers for publication.  And who knows?  It just might work.

Tuesday, January 17, 2012

I'll Drink to That

Most of us who care about such matters are probably quite familiar with the idea that moderate alcohol consumption can be a healthy and life-extending activity.  But I still couldn't help my giddiness when I came across an article on the Yahoo! featured news feed that describes the health benefits associated specifically with beer.  Some of the 10 health benefits the author describes are common to all alcoholic beverages, but are greater for beer than for other alcoholic drinks like wine and spirits.  And some of the benefits truly are specific to beer alone.

So the next time you raise a pint to your lips, take comfort in the fact that you're drinking that pale ale for recreational AND medicinal purposes!

Friday, January 13, 2012

My Phone Just Got Way Cooler

This is awesome.  A computer scientist at NASA's Jet Propulsion Laboratory (JPL) has developed a smartphone app that allows users to see images from the latest download link of the Mars rover Opportunity as soon as they're available.

If you're interested, the app is called Mars Images and it is developed by PowellWare.

Yes, I've already downloaded and tried out the app.  Yes, it is wicked cool.