I am using a Hewlett Packard ScanJett IIc, about 800 dpi with some
interpolation,
color / bw. This is an "older" model, so I bought a used one for 500 sFr.
(swiss franks).
- OCR even for small printed text (as in journals) is satisfying with OmniPage.
- Microscopic slides *can* be scanned, resulting in about a 30 fold
magnification.
Personally I am very satisfied with this device. Good Luck, Wolf.
wschweitzer@access.ch (Wolf Schweitzer)
K.-R. Peters wrote:
Optimal scanning of negatives requires that the negatives are exposed 1-2
stops more than for ordinary photographic printing (high lights should be
"covered" and not be empty, dark areas should be very dark. Good scanners
can handle more than 3.0 optical density which is "very dense" for a
photographic negative). Also the scanning procedures must be adapted in
order to take advantage of the full contrast transfer function of the
negatives as well as the scanner. I am in the process of putting a report
together at my WWW site on our experience with 8-bit versus 12-bit negative
scanning.
Best regards Klaus
Klaus-Ruediger Peters, Ph.D.
e-mail: Peters@BSAC.UCHC.EDU
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
we have partially overcome this problem by overlaying negatives with
photographic contrast filters or neutral density filters. This may not be
appropriate for very high res. work but is no problem for video display and
printing to a laser printer
Greg Erdos
E-mail: gwe@biotech.ufl.edu
K.-R. Peters wrote:
Optimal scanning of negatives requires that the negatives are exposed 1-2
stops more than for ordinary photographic printing (high lights should be
"covered" and not be empty, dark areas should be very dark. Good scanners
Greg Erdos responded:
we have partially overcome this problem by overlaying negatives with
photographic contrast filters or neutral density filters. This may not be
appropriate for very high res. work but is no problem for video display and
printing to a laser printer
Greg Erdos
E-mail: gwe@biotech.ufl.edu
Thanks Greg, you make an important point concerning acquisition and display:
The application of contrast or neutral filters in photography shifts the
brightness (level) or contrast (slope) of the image data to a range at
which the eye is more perceptive (details in high lights may be preserved,
but reduced in the shadows or visa versa, or both may be compressed). These
procedures do not produce more "image detail" than the negative contains
but modifies the display of the details. If during image acquisition
(negative exposure) the highlights in the negatives were underexposed (or
the shadows overexposed) then the possibly lost detail information can not
be recovered, neither analog nor digitally.
It is therefore important (for both analog as well as digital imaging of
the negative) to the set the brightness level of the negative so that it
captures as much information as possible. Generally, the contrast transfer
function (slope) is not changed, i.e., through variation of developing
conditions or change of film/developing combination. But why don't we
normally care much about optimal exposures (or acquisition)?
Photography (analog) had long accepted that there is more information in a
negative (raw data) than the eye can "see" ("image" being that part of the
displayed image data which the eye can perceive and recognize). It
developed many useful tools for enhancing the contrast of certain image
components of the negative so that they become visible, but consider our
following findings. Measurments of the intensity ranges of contrast
patterns in digitized EM negatives and the contrast ranges required for
visual display of these contrast patterns (as images) indicates that an
optimally exposed TEM negative has an information depth of approximately 12
bit, or a 12-bit contrast resolution whereas the "image" has merely an
approximate 6-bit contrast resolution. We find in digital image data from
nearly all microscopies that the detail contrasts (structures of lowest
contrast levels) occupy only 1-10 % of the overall contrast range of the
image data whereas we need about 25% of the contrast range of an image for
visual recognition (not perception) of a contrast pattern (in an amorphous
environment). This means, most of the low-contrast data components (which
constitute the high-resolution details) are not visible in a conventional
image of the data. Unfortunately, we have adapted to this fact and tend to
acquire images at an insufficiently low contrast resolution level equal to
that of our visual system because we are not missing anything in the
"empty" high-lights or empty shadows although our microscopes can acquire
images at much higher contrast resolution. On the other hand, these facts
underline why digital acquisition (from the imaging sensor or from the
negative) should be done at a 12-bit level instead of an conventional 8-bit
level. Many manufactures of acquisition and processing equipment start to
provide a 12-bit "output" level, 12-bit scanners are now offered at catalog
firms, and Photoshop is now available for PCs and Macs with 12-bit TIFF
capabilities (version 3.04).
The basic idea of scanning negatives is to "preserve" all information of
the negative with a linear transfer function, irrespectively if the eye on
the negative or print can see it or not, and then use digital imaging for
the display of all the available image information. Thus, when exposing a
negative for digital scanning, we should capture the contrasts of interest
with the largest possible contrast range. Since good scanners can penetrate
the darkest black of a negative (max. OD = 3-3.5) capturing the details in
the shadows, we should expose more than conventionally done in order of
acquiring also as much detail as possible in the high-lights.
Additionally, one should consider that laser printing (HP LaserJet 4
providing 5-bit gray levels and 100 lines/inch) combined with the
LazarPrint expansion can print 8-bit gray levels at 300 lines/inch, thus
provides a good output for detail rich images at the 1Kx1K level (I tested
recently several printers and reported the results in my home page).
Klaus-Ruediger Peters, Ph.D.
e-mail: Peters@BSAC.UCHC.EDU
In response to Klaus Peter's eloquent plea for 12-bit versus 8-bit scanners:
While I would not want to be thought of against precision, it must be
admitted that there are some limitations to using 12-bit data, namely
greater storage (and display?) requirements. So one should consider this
step carefully.
Assuming that it is done correctly, 12-bit data is digitized to 1 part in
4,000 while 8-bit data is digitized to only 1 part in 256. Therefore, to
make proper use of such precision one must have data of similar precision.
Although many considerations can reduce the precision of recorded data:
measurement noise, low contrast, it can never be better than the
statistical limitations placed by quantum mechanics on the number of events
counted (grains of silver (assuming that they are all of the same size
which whey aren't)/pixel or photons/pixel or electrons/pixel). Clearly,
this all depends on the size of a pixel: larger pixels imply the chance to
count more quanta (but they also mean lower scanner resolution) so you may
need less intensity resolution if you have greater real (non interpolated)
spatial resolution.
Now it is clear that, for instance, in STM, where a 0.05 nm height
resolution can be detected and the piezo may have a height sensing range of
many microns, there is no difficulty in obtaining 12-bit data (or even
16-bit data) although you may have trouble displaying all of this "depth"
to a human observer at one time. Likewise, CCD sensors having noise levels
of +/- 3-4 RMS electrons/pixel and full-well signal levels of 300,000
electrons/pixel easily satisfy the 4,000:1 (more like 100,000:1 possible)
requirement as long as you use a long enough exposure to actually record at
least 20,000 electrons/pixel. However, in confocal microscopy, 256
photons/pixel is often quite a high signal and digitizing from a color
slide of a fluorescent image recorded on high speed film (depending on
original magnification and pixel size. Remember, 1200 DPI implies 20 micron
pixels.) one may find it difficult to find even 10 distinguishable levels.
So far we have only spoken of linear digitization (as is appropriate to
scanners which usually make every effort to be linear). However, for
signals degraded mainly by statistical noise and recorded by the direct
digitization of electron signals, the separation between "meaningful" grey
levels (those separated in intensity from neighboring levels by an amount
at least equal to their standard deviation?) the difference between the
first two such levels (1 event/pixel and 4 events/pixel) is 3 event/pixel
whereas that between the 15th level and the 16th is 31 events/pixel. In
other words, if we are only interested in recording the INFORMATION in a
signal limited only by quantum noise (SEM? Confocal?), we could first take
its square root and then digitize this. This could be done using only one
half of the number of bits that would have been necessary to preserve the
information in a linear signal and each SQRTBit would be a "real" grey
level.
All this said, one must admit that getting real 8-bit data requires more
than the use of an 8-bit DAC (0.4% illumination stability, low-noise
detector, freedom from digital electronic interference, proper bandwidth
for sampling rate in both the electron and optical parts of the information
path, etc) and many scanners may not provide the performance they claim.
This might explain much of the difference claimed to exist between 8-bit
and 12-bit results.
(To any owners who have read this far: have you any MEASUREMENTS on scanner
performance on known images?)
SEM might provide a good case in point: The SE signal variation associated
with small features is often less than 1% of the total signal. As "seeing"
a small feature with only 1% contrast requires collecting at least 1/0.01
x0.01 = 10,000 electrons/pixel, it might seem worthwhile to use 12-bits to
preserve these small variations. However, unless there are "holes" in your
specimen from which virtually no signal is obtained (i.e. if your signal
does not have "important" high contrast), little would be lost if one
digitized only the 256 levels nearest in intensity to those of the small
feature and a positive improvement would be gained (all the information
that could possibly be coded in up to 65,000 detected electrons vs. 10,000)
by digitizing the square-root of the signal into only 8 bits. In either
case you would have to "process" the signal before you displayed it on the
screen.
Just some thoughts. Sorry that they were so long but I felt a trend to
Digital-One-up-man-ship..
.
Jim Pawley
JBPAWLEY@FACSTAFF.WISC.EDU
To all,
Sample depth:
10 bits for grey
30 bits for colour
Scan mode: one pass
Scanning speed:
grey 4.5 ms/line
colour 10 ms/line
Scanning area: 316x355 mm (8.5"x14")
I would like to add a couple of comments to the recent thread about
negative scanning.
Macintosh system
We use the HP IIcx flatbed which is no longer available, but is now sold
as a HP 3c (<$1000). It is a very capable scanner, but you have to buy the
transparency adapter for an extra $600. As a WIntel applet the twain
software is very solid but they haven't delivered a 32bit driver yet for
Win95/NT ... the 16bit still works however.
Back a few weeks to our discussion of flat bed scanners. It was noted that
negatives need to be 1-2 stops overexposed for the transparency adapters to
work properly.
UMAX has come out with a new version of there software that operates
under Windows '95 that allows one to adjust the lamp intensity. I have not
tried it. However one assumes that this would then enable one to compensate
for light or dark materials that fall outside the range of the automatic
settings
Greg Erdos
I got a number of good responses on my question regarding flatbed
scanners. Everybody seemed pleased with the particular one they
owned--there were no clear favorites. A couple of tips: 1) Make sure
your computer has the right output. All of the scanners I have looked at
have a SCSI 2 output while my 2.5-year-old Mac only has a SCSI. I have
been told that I have to upgrade my computer in order to even hook it up to
a SCSI 2 scanner. I'm still investigating this. 2) Make sure you get the
software you need to manipulate the scanned image or text. A lot of
scanners come with software bundles. 3) Look into warranties. Some
devices have none--others are up to 2 years (longer?). 4) Photoshop
comes in two versions--LE and 3.1. The latter is more powerful (and
expensive) than the former. 5) Transparency adapters and document feeders
are usually extra. Both can be useful.--if you need them. 6) Read the
first response (from
Bob
________________
From: sco.umc2@Mail.health.ufl.edu
One user's opinions:
1. Consider the media you will be scanning. Some scanners do
better at transparencies than others (nikon has a slide scanner
for 3K$), some are designed for large format (Umax has a 17 x 12
inch for 7k$), some do black and white on the cheap (HP has one
B&W for $400).
2. Consider the destination of the image. There is no use
buying a 30 bit high definition scanner if all you will do is
newsprint. A 300dpi 256 gray scanner goes a long way with laser
printers and costs $400.
3. Consider the resolution you need. If you are going to scan
stamps that are 1 inch, and display them at poster size, you need
a very high res scanner (1200 dpi or more) if you are going to
scan 8 x 10 positives and display them in a small window, then
600 is plenty, 300 adequate.
4. Consider the speed. Some scanners take 30 seconds to scan
one page. This can be a real pain if you have any number of
images to scan. Some are available with a document feeder, which
is a nice thing to have, but not if all your scans will be of
pictures (which must be hand fed anyway)
"Single pass" scanning means that all 3 colors (red green blue)
are captured simultaneously--this is faster (HP scanjet 4 offers
this)
5. Real Res. Most scanners interpolate the dpi at high res.
This is ok, but non-interpolated scans are better. Be willing to
pay more for a hardware 600dpi than a software 600dpi.
__________________
Sender: bob@befvax.uchicago.edu
What resolution do you need. Many of the inexpensive scanners have a very
small numerical aperature which leads to line broadening. So a step
size of (for example) 5 microns will not resolve a 5 micron line in
single (or two) pixels but rather 10 or more. The requirement for a
large numerical aperature coupled with dimensional stability is
what makes high resolution cost so much.
Bob J.
______________
Response from John Bozzola:
We use a Mac IIci attached to a LaCie 600 dpi color scanner (it's
equivalent to an Epson 300) to occasionally digitize prints. It cost $1,800
- a similar unit may now be purchased for around $600. I have used it for
over 3 years now with no problems whatsoever. 97% of the scanning is done
in the bw mode set to no more than 300 dpi. The program most often used to
drive the scanner is Adobe PhotoShop. As an OCR program, I use WordScan
Plus. It's OK, a bit slow, but it is also 3 years old and a newer version
may be better. I rarely use this program. However, when the documents are
of high quality (typed characters no smaller than 9 point) then it is a
great time saver. There are better OCR programs out there than this one.
_________________
Our Graphics Artist uses a Macintosh computer with a Hewlett Packard scanner
which he likes very much. The one we have is color and has a 400 optical
DPI, although the new Hewlett Packard has a 600 optical DPI. It comes with
Deskscan software and a limited version of PhotoShop. If you want to use
color, though, you need to have the full version of PhotoShop.
Hope this is helpful.
Kathy Stangenberg
Ted Pella, Inc.
_______________
I have a AGFA StudioScan IIsi scanner with Transparency module. I
think that it is a very good scanner. I using it every day.
Some technical data:
- Max. res. 400(H) x 800(V) optical
2400(H) x 2400(H) ppi through interpolation
MAC PC
SM=Speed mode (in seconds)
SM QM SM QM
Preview colour 16 16 15 15
A4 colour 200 ppi 54 54 32 39
A4 colour 400 ppi 96 104 86 126
15x10 cm colour
400 ppi 44 54 30 38
A4 grey 200 ppi 17 18 12 12
A4 grey 400 ppi 39 42 39 65
A4 line art 400 ppi 20 34 20 34
QM=Quality mode (in seconds)
Software:
- OmniPage Direct OCR
(I suggest you to buy Recognita OCR software, because it is the best as
I think)
- FotoTune
- PhotoShop LE
Price: Scanner + Transparency Module = 250.000 HuF => 1.700 USD
dr. Peter Kasa jr.
E-MAIL: KASA@PHARMA.SZOTE.U-SZEGED.HU
________________
From: MELSEN
Regards, Skip
___________________
We are running a Umax Power-look with a transparency scanner for doing
negatives. It came with all the right software including Adobe Photoshop
for either PC or MAC. I think it was about $2600. directly from Umax. We
have been very happy with it so far. Another lab has the same scanner
running on an SGI Indy. Apparently the software is more tricky on that
platform but the results have been very good.
Greg Erdos E-mail: gwe@biotech.ufl.edu
______________________
We have an HP Scanjet 3c/T scanner on a Powermac 9500
used for image analysis and presentation purposes. It is
a superb accessory. You can scan virtually anything that
is 8.5 X 11 or smaller with it, although it does not substitute
for a good slide scanner. Since it has the transparency adapter
gels come out very nicely. It has its own miniprogram for
image adjustment, but if you are doing serious work we have
an Adobe suite (Illustrator, Pagemaker & Photoshop) installed
on the Mac and that is what just about everyone uses. For many
types of text (but definitely not all) you do not even need OCR.
If you can afford it, it seems to be the way to go. I am a user and
do not have any financial connection to Hewlett - Packard.
Bruce Cutler, Microscopy Laboratory, Univ. Kansas, Lawrence.
_________________
We have experience with some HP-IIcx's. One is on a Mac, the other on a IBM
PS/1. Both seem to work quite well. They ran about $1000 over a year ago. I
think they support 1200 dpi.
They came with minimal software. The software allowed scanning images well
enough. But optical character recognition required third-party software.
That may all have changed.
Warren E. Straszheim
E-Mail: wes@ameslab.gov (or: wesaia@iastate.edu)
___________________
From: wschweitzer@access.ch (Wolf Schweitzer)
I am using a Hewlett Packard ScanJett IIc, about 800 dpi with some
interpolation,
color / bw. This is an "older" model, so I bought a used one for 500 sFr.
(swiss franks).
- OCR even for small printed text (as in journals) is satisfying with OmniPage.
- Microscopic slides *can* be scanned, resulting in about a 30 fold
magnification.
Personally I am very satisfied with this device. Good Luck, Wolf.
______________
From: smiller@umr.edu (Scott Miller)
We use a UMAX 1260 color flatbed scanner, which will scan to 3000 dpi, and
we love it. It is a three pass color scanner, but the speed isn't slow
enough to justify another $1000 for a one pass scanner. It works as a
plugin to Photoshop.
Also, we use OmniPage Pro for OCR, and again, it's great!
Any questions, just email me.
Scott
________________
From: Peters@BSAC.UCHC.EDU (Klaus-Ruediger Peters)
Bob, we are using extensively flatbed scanners for digital imaging of our
negatives (fluorescence and histology color LM, TEM and old Polaroids from
my FSEM). My suggestion: Buy an Agfa Arcus II for true 8-12 bit graytone
or 24-48 bit color "output" in TIFF. AGFA is experienced, has excellent
color handling and will be around for a long time for support. The street
price of US$ 2,000 (any US catalog company, i.e., The Mac/PC Zone
1-800-248-0800) includes a "full version" of Photoshop 3.04 which reads and
writes 8-12 bit Tif files. TIFF is the MSA standard. Both versions (PC and
Mac) of Photoshop 3.04 are now available and allow us to work with 12-bit
Tiff's (at my microscope on a PC and at my networked office with a Mac).
The scanner comes with AGFA's FOTOLOOK acquisition software which is opened
from within Photoshop: Files-Acquisition.
Please consider: Not spatial resolution but "contrast resolution" is
important for the acquisition of digital image data, i.e., if you read more
intensity steps you can work with more intensity levels per pixels and can
"see" smaller contrasts. Our experience is that all microscopes can deliver
12-14 bit contrast resolution. The jump from 8-bit to 12-bit gives you an
increase in contrast resolution of 1:16 which is adequate for utilizing the
full range of contrasts found in (TEM, Polaroid) negatives. Their is
already some software out for the handling of 12-bit image data and I
believe that soon many other software packages will available for working
at the level of 12-bit contrast resolution already available in many
microscopes, e.g. AFM microscopes, good CCD cameras for TEM and several SEM
acquisition systems. Even, if you cannot handle 12-bit data at this time
and may have to wait for an upgrade of NIH image, a foreseeing investment
in adequate hardware will pay of very soon when 12-bit contrast resolution
will have a common place in microscopy imaging.
Optimal scanning of negatives requires that the negatives are exposed 1-2
stops more than for ordinary photographic printing (high lights should be
"covered" and not be empty, dark areas should be very dark. Good scanners
can handle more than 3.0 optical density which is "very dense" for a
photographic negative). Also the scanning procedures must be adapted in
order to take advantage of the full contrast transfer function of the
negatives as well as the scanner. I am in the process of putting a report
together at my WWW site on our experience with 8-bit versus 12-bit negative
scanning.
_____________
From: "Fermin, Cesar"
If black and white prints are to be scanned, the Apple one Scanner (up to 1200
dpi) cost now less than 700 dollars and is very good with OFOTO software.
Equivalent scanners (e.g. LaCie are just a good), but I am not sure about PC
equivalent and would certainly like to know the outcome of recommendations.
Images in the page below were scanned with the Apple one scanner at 300dpifrom
black and white prints without any manipulation (filtering, etc).
Several people have mentioned using moderately priced flat-bed scanners
with transparency adapters. My evaluation of one of these (Epson Scantastic)
was that it was useful for quick prints of light (density 1 or less)
negatives to show qualitative microstructure. This unit had a
non linear response to density, especially over 1. This made the output
unsuitable for quantitative analysis and often resulted in "posterization",
where large areas with visible contrast differences were all mapped to
the same gray level. Check for this by scanning a density step tablet.
Scanning periodic features in the negative (i.e. lattice images) resulted
in moire patterns (check the FFT of some of your images).
As a result, we chose not to purchase this scanner and added a new
PC interface to our old Optronics P1000 rotating drum scanner. With
the addition of a new module for the log amplifier that permits a wider
range of gain and DC offsets, we can select linear ranges of density
of 0.5, 1.0, 2.0, 3.0, and 4.0 with a variable offset of up to 1.5
density units. (This all was supplied by CSI, a small company in England).
This provides the ability to get the most significant 8 bits of data per
pixel and is free from interference effects.
For the highest resolution, we send the negatives to another lab which
has a Perkin Elmer flatbed microdensitometer. These scans are very slow,
but have the potential of very high resolution (we have scanned down to
5 microns t0o be certain we oversampled the film).
Best Regards,
John
John R. Minter, Ph. D.
email: minter@kodak.com
I was leafing through Macworld the other day and realized that they had
reviewed several scanners in the last 6 months. The recommendes ones were
(4 or more stars out of 5):
Flatbed scanners:
HP Scanjet 3c
30 bit dynamic range, 600 dpi optical resolution, list $1179,
street ~$700
208-323-2551
PixelCraft Pro Imager 8000
30 bit, 1200 dpi optical, list $13k
510-562-2480
35 mm negative scanner:
Polaroid SprintScan 35
30 bit, interpolated 2700 dpi, list $2495, street ~$1600
-Kirk
krogers@materials.ecn.purdue.edu
If black and white prints are to be scanned, the Apple one Scanner (up to 1200
dpi) cost now less than 700 dollars and is very good with OFOTO software.
Equivalent scanners (e.g. LaCie are just a good), but I am not sure about PC
equivalent and would certainly like to know the outcome of recommendations.
Images in the page below were scanned with the Apple one scanner at 300dpifrom
black and white prints without any manipulation (filtering, etc).
Cesar D. Fermin, Ph.D
Fermin@tmc.tulane.edu
Regarding dye-sub printers ... I suppose you realize they are color
printers and you pay $extra$ to print on color stock (<$3/pg) in spite of
the image being monochrome. The option does exist for grayscale ribbons
(<$2/pg), but they are more than a hassle if you use color sometimes and
want to use grayscale at times. We ^do^ use a Codonics ethernet printer
which has the Kodak dye-sub engine ... and we can reccommend it ... it is a
different type of ethernet printer ... let me know if you want to know more
about it. As another option there are Ag salt laser printers available which
print grayscale at 256dpi which are ^not^ dithered ... ie, ^true^ 256 shades
of gray. They are expensive (<$14k), but the cost is less than a $1/pg.
Regarding, archival storage of image files ... you should $invest$ in
magneto-optical. We chose to go with a Fujitsu 230MO drive (<$700) for which
the replacable media costs <$30 and can be found for near $20. The other
option which we now wished we could have afforded would have been to go with
1.3Gb drives for which the drives are more expensive, but the media costs
are less expensive (per Mb). These MO drives offer the freedom of
write/delete ..., a third option would be write once CR-ROM drives for
archiving ... again the drives are expensive but the media is less than $15
for 600Mb. Lastly, in this regard and to mention alternatives, eg Zip
drives, some people would imply they shouldn't be used for "archiving" as
the magnetic media shouldn't be trusted to any degree more than floppies or
hard drives for occasional and intangible influences. On the other hand, MO
drives require an annealing temperture to change a bit, which also means
they write more slowly but they do read quickly.
Hope this helps ..
cheers, shaf
Michael Shaffer
mshaf@darkwing.uoregon.edu
E-mail: gwe@biotech.ufl.edu
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