scanning microscope slides

[jamie boyd]

Hi:

Has anybody had any experience with this?

Rather an esoteric question, perhaps. For those who don't know, these
are thin (50-100 microns) slices of tissue embedded in a clear viscous
medium and sandwiched between thin plates of glass. Surface area of a
slide is 1 -2 inches by 3 inches and, like 35 mm slides, they are meant
to be viewed with transillumination. For high power stuff, we have
cameras (now digital ones mostly) mounted on microscopes. But getting a
good low power image of large portion of section can be more difficult.
A few people have published pictures made by putting the slides on a
flat-bed scanner. I have tried this, but I have a lousy scanner, and
have not been satisfied with spatial resolution nor dynamic range
compared to film.

Spatial resolution should be solved by getting a better scanner with
higher optical DPI. For what I want, about 10 micron resolution will be
more than sufficient, and if I've done the math right (1/(.010 mm * 25
mm/inch) = 2500 DPI), that's within the range of current machines, even
moderately priced ones.

Dynamic range is the more problematic, I think. I know there are
inexpensive 36 bit scanners available now. Are they substantially better
than 24 bit scanners? In some cases, colour is not important, and I
would really like 16 bit greyscale. Do any scanners do this? Also, just
having the resolution is not enough, the quality of the the A/D
conversion is important. If the extra 12 bit resolution is just noise,
it's not doing any good.


Suggestions re. what scanners to buy, or hints on getting good images
much appreciated.

jamie

--
Jamie Boyd
Dept. of Biological Sciences
Simon Fraser University
phone: 604 291 4442
http://www.sfu.ca/~jboyd/

 

[Don]

Has anybody had any experience with this?

No experience, but...

Suggestions re. what scanners to buy, or hints on getting good images
much appreciated.

....I remember reading something about it in the manual. Hold on.

fx: Pitter-patter of little feet: TAP, TAp, Tap, tap... (pause)
...tap, taP, tAP, TAP! OK, I'm back! ;o)

Seriously though, NikonScan4 reference manual says this:

--- start ---
Scanning Glass Microscope Slides

Turn Digital ICE4 Advanced off when scanning glass microscope slides
in the FH-G1 or FH-8G1 medical holders (available separately). Digital
ICE4 Advanced may fail to produce the desired results with glass
microscope slides.
--- end ---

FH-8G1 is for the Nikon 8000 ED and 9000 ED models, while FH-G1 is for
the CoolScan IV ED, CoolScan V ED, 4000 ED and 5000 ED Nikon models.

ICE is dust and scratches removal based on a separate infrared light
source scan and, besides Nikon, also available on a Minolta scanner.

Most film scanners today are in the 14 to 16 bit dynamic range. I
think that makes a huge difference (previously I had a 10 bit film
scanner). Actually, I'm scanning each (film) slide twice in order to
extend the nominal 14 bits of my scanner (CoolScan V ED) to an
effective 17-18 bit range. Do note that this is all for film and I
have no idea how relevant this would be for you.

You may also want to check the sites of the other "usual suspects"
(Minolta, Canon, HP... or whoever else makes film scanners) and see if
they are as explicit about scanning biological slides as Nikon.

One last thing is that Nikon is the only manufacturer to use LEDs as a
light source rather than conventional illumination. I don't know how
relevant this is for you but if you check the archives I wrote a
message about some pros and cons of LEDs just a couple of days ago.

Don.