NetNotes
solution as follows: 25 ml conc. HCl, 175 ml distilled water, 50 ml 99%
works well. Though most programs such as this are meant to stitch
acetone. Of course, add the acid to the water, and then add the acetone.
together consumer-level JPEG photos into a panorama, this particular
I sonicate copper or nickel grids, mesh or slots, for about 30 seconds
one can use planar / flat field TIFFs - which is great for microscopy. ICE
in a 25 ml beaker with about 10 ml solution. Then I pour that off, and
is free of charge but is officially unsupported by Microsoft. It appears to
sonicate once with 99% acetone as a rinse. Then invert beaker onto
be stable in my limited testing. It is available for 32- and 64-bit Windows
clean filter paper to air dry. The grids usually stick a bit to inside of
systems from: http://research.microsoft.com/en-us/um/redmond/
beaker but will fall off when they dry. I do this each day before I begin
groups/ivm/ICE/ There is an Image Composite Editor forum that has
sectioning. The copper grids get so clean - fresh copper exposed - that
a few support notes describing the various functions and settings of
they may oxidize enough overnight to need cleaning again even just
the program (link at the bottom of the ICE page): http://community.
a day later. I also clean grids this way before any coating with films,
research.microsoft.com/forums/112.aspx http://community.research.
like Formvar or Butvar. This method of cleaning has worked for me for
microsoft.com/forums/t/2002.aspx ICE appears to be faster than the
many years and sections stick to the grid. Oh, I also pick up floating
MosaicJ plug-in for ImageJ, though the latter gives you more flexibility
sections from above onto the dull side of the grids. Others report good
and options in layout and is documented in the scientific literature. I’m
results picking up from below the floating sections, or onto the shiny
not sure which algorithms ICE uses. http://bigwww.epfl.ch/thevenaz/
side of the grids. Others report good results cleaning grids by quickly
mosaicj/ Marc Takeno takenomm@u.washington.edu Fri Jun 5
flaming them in an alcohol lamp flame. In this new age of solar energy,
In our lab, people now use PS CS4, with - I assume - further
I have not yet tried cleaning grids by concentrating the sun’s rays with
improved function(s) for image stitching / merging. At least, the results
a 4” hand lens onto grids resting on a clean, refractory surface. But
are very good. Photomerge. TEM: this very much depends on the
if it worked, that would be so green! Someone ought to try this. Gib
magnification. It works +/- easily and automatically (Photomerge) with
Ahlstrand ahlst007@umn.edu Fri Apr 24
images taken in medium / high magnification mode (above 3000x).
I noticed that after the advent of thin bar grids, sections didn’t
In low magnification mode on our CM12, images contain obvious
stick as well, probably because there was less surface area for sections
distortions, preventing perfect alignments. People who are well trained
to adhere to. Like Pat Common, I just put them in a 50 degree oven
in PS CS4 can use built-in functions for correcting these distortions,
and never lose sections. 30 minutes works but we’ve left them in there
before the images are merged. Not easy, but works satisfactorily. I just
inadvertently for several days, and they are fine. No pre-cleaning is
checked PS CS4 again: “Photomerge” even includes filters (“layout”)
necessary. An absolute ethanol dip does seem to minimize the tendency
offering some preliminary correction of distortions. Reinhard Rachel
for sections to “run away” and also cuts down on what I call the Jell-O
reinhard.rachel@biologie.uni-regensburg.de Fri Jun 5
water effect. Mary Gail Engle mgengle@email.uky.edu Mon Apr 27
Gatan include ‘Digital Montage’ in the software available for their
cameras that seemed to work well stitching together the TEM images
Specimen Preparation: [it was only used with their camera, albeit with an offline workstation].
sharpening carbon rods But it was fantastically expensive [well the camera was and it came
File this Tip of the Week under “Okay, so why didn’t I think of this as a package]. See: http://ftp.gatan.com/products/digital_imaging/
before, dummy?” We have one of those hand-held carbon rod sharpeners products/Digital_Montage.php . Not used it since I left UCL a couple of
that require you to twist the rod manually in order to get the narrow years ago though, but it went down well with the TEM users. The software
tip needed for evaporating. They are hard and uncomfortable to use, balances intensities between images as well. The Montage image files
often break the tip off just as you’re finally getting it to the length you were large though. I always found Photoshop CS2/CS3 Photomerge
need, and just generally a pain. But I could never bring myself to spring to be pretty awful at photo-stitching photographs and I’ve long
for the hundreds of bucks for a decent sharpener, especially considering abandoned it. I’ll try the CS4 version next time to see if it has improved
the volume of evaporating we do. As I was cranking away this morning, any. In fact the software that came with my camera ‘Olympus Master,’
breaking tips and saying bad words, I remembered that we had a Dremel after you paid for the Pro upgrade, worked far better for camera photos
tool in the next room. Took that carbon rod, put it in the drill bit chuck, so I still stick with that. It can’t get it right every time and so a manual
turned the tool on at its lowest speed, inserted the rod into the sharpener edit to taste is often required. Camera lens distortions and positional
and had my tip in about 17 seconds. Many of you probably had this one errors are presumably worse than that found in ‘flat’ 2D TEM images.
figured out a while ago, but if not, here it is. I now have the will to go on Try things like: copy & paste badly affected areas, and Free Transform,
evaporating. Randy Tindall tindallr@missouri.edu Fri Apr 24 and Transform ‘Distort’ etc. to overcome poor stitching at the overlap
A Sears Craftsman variable speed 3/8th inch drill works just as [plus see the link below]. Image analysis packages like MetaMorph &
good, has more low speed range, and takes any size carbon or graphite AxioVision seem to go for the more conservative Montage, where the
rod (1/8” to 1/4” or more). I made a sharpened rod one inch long that ‘overlap’ edge is left as is, but I don’t see much problem ethically with
way with just a Sears drill and a manual sharpener. I also used a fast very minor photo editing to get it to look nice assuming nothing of
turning lab scale miniature lathe years ago but the drill works better importance is edited away or added. Generally though ‘looking nice’
and is smaller but heavier than a Dremel tool. Kiss sore and black is just for the web or presentations, being aesthetic, and is often of no
fingers goodbye! Paul Beauregard beaurega@westol.com Fri Apr 24 particular scientific importance. You can buy various similar photo-
stitching panorama software, all largely aimed at photographers
Image Processing:
though: http://www.cs.ubc.ca/~mbrown/autostitch/autostitch.html
image stitching [seems well regarded] http://www.ptgui.com/info/photo_stitching.
Photoshop CS2’s Photomerge function works well on my LM flatfield html http://www.vrtoolbox.com http://www.easypano.com/photo-
images, but with TEM images sometimes there are misalignments in some stitch-software.html http://www.panobuilder.com/index.asp http://
areas. I assume this is due to spherical aberration in the TEM images. www.vextrasoft.com/rasterstitch.htm This is just a selection, prices
Can any of the other software options out there detect and correct for vary, and all can’t perform miracles, although the results can be very
spherical aberration? Ralph Common rcommon@msu.edu Fri Jun 5 impressive after a minor edit or smudge here and there. I tried a few on
I’ve been experimenting with Microsoft’s Image Composite Editor demo, but my Olympus E500 SLR camera’s Olympus Pro* software did
(“ICE”) to make mosaics of microscopy images, and it seems that it as well so I never bothered ‘upgrading’. Often it’s brightness differences
64
www.microscopy-today.com • 2009 September
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