Subject: Help! [Microscopic images directly to a computer file]

From: SG <[email-masked]>
Date: 14 Mar 1996 15:35:47 GMT

I would be grateful for help from somebody who has experience of 
making computer images of microscopic objects using a digitising camera 
directly attached to a light microscope (and thereby avoiding the need in 
making conventional photographs). 

I have got some manufacturer's prospectuses about CCD cameras for microscopes
but I would like to hear from the people who actually use those cameras 
whether it is possible (and practical!) to use this way for making images of 
biological preparations (cells and tissues) with "publication" quality.

Sergei Gutnikov, D.Phil.
Department of Experimental Psychology
Oxford University
UK                                          [email-masked]

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From: "K. D. Ham" <[email-masked]>
Date: 14 Mar 1996 17:39:36 GMT

>UK                                          [email-masked]

If you already have a normal video camera that is attached to a microscope, you may 
want to check out a frame grabber from Play Inc. (www.play.com) I think it is called 
Snappy and costs less than $200US. I haven't used it, but you can download a demo 
program that demonstrates picture quality (impressive on screen). By some 
proprietary algorithm, they claim to be able to far exceed the TV resolution you 
expect from such a camera. By printing those images, it should be possible to 
evaluate whether they would be publication quality. I believe they support both PAL 
and NTSC video sources.

I hope this helps.

Kenneth

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From: [email-masked] (Steve Gage)
Date: Thu, 14 Mar 1996 23:19:13 GMT

>UK                                          [email-masked]

It is very possible and extremely practical to capture microscope
images from a CCD camera directly to computer. I do it every day! I
have a Cohu CCD camera in a Zeiss inverted microscope connected to a
Mac Quadra 800 running IPLab Spectrum from Signal Analytics. Above and
way beyond generating publication quality images, the image analysis
and manipulation you can do with this program are truly amazing! I'm
sure similar programs exist for Intel-based machines.

My work mostly involves analyzing growth rates, shapes, areas, etc. of
neurite growth cones in vitro, and I use the above-described system
pretty heavily, so if you have any particular questions, I'd be happy
to try and answer them in the newsgroup (I found your msg in
sci.bio.botany) or via email.

Regards,

Steve

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From: [email-masked] (rmw)
Date: 14 Mar 1996 17:42:10 GMT

In article <[email-masked]>

> UK                                          [email-masked]

Sergei, 
It's done all the time--in fact, there are probably more digital
photos taken these days than film photographs.  You have to have
a computer and a frame-grabber, but that's it.  Well, on second
thought, you also need a photographic-quality printer somewhere
to get a "publication" quality print.  The better the CCD, the 
better quality the image.  Why don't you ask the CCD companies
for a demo?

--Randy
CCD, the better the picture.  Why don't you ask the

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From: Jerry Clayton <[email-masked]>
Date: Thu, 14 Mar 1996 22:30:22 -0700

I second steves comments!  I too use a Cohu 4900 series camera and my 
frame grabber is a Scion board with expandable memory.  Total price of 
camera and board was approx. $2000 (US). I find that by using Apple 
MacIntosh computers (Good used one are available that will do the job) 
greatly facilitates digital microscopy.  In addition there is FREE 
software available from NIH called "IMAGE" by Wayne Rasband.  You can 
download it from Zippy.nimh.nih.gov.  This level of ccd camera provides 
very good quality for the price!  Unfortunately the next level of 
resolution (i.e. direct digital ccd cameras) are still a lot more 
expensive.  This combination of camera, card and software has served me 
well for several years (Scion even takes old card trade-ins if you 
eventually upgrade to a spiffier frame grabber) and for grabbing and 
analysing images "IMAGE" can't be beat.  Glad to give you more details 
on my experiences, just drop me an e-mail.  I also agree with steve in 
that the limiting factor can be a good quality photo printer (somewhat 
expensive).  Sharing costs amongst several users often works or (if your 
low on resources but still want to start into this type of image 
production) commercial image printing sites will let you send them your 
completed images via the internet and then send you a print.  
-- 
Jerry Clayton
[email-masked]
Dept. of Neurology
University of Colorado Health Sciences Center
Denver, Colorado USA

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From: David W Walker <[email-masked]>
Date: Fri, 15 Mar 1996 11:58:07 +0000

>directly attached to a light microscope (and thereby avoiding the need
>in making conventional photographs). I have got some manufacturer's
>prospectuses about CCD cameras for microscopes but I would like to
>hear from the people who actually use those cameras whether it is
>possible (and practical!) to use this way for making images of

Hi

May also be worth asking around other Depts at Oxford for on-site
advice. Somebody in another field maybe using a setup similar to the one
you may be interested in, and may be willing to produce printed output
for one of your specimens before you decide on a purchase.

regards

Dave Walker
----------------------------------------------------------------------------
 David W Walker    EMail [email-masked]                 
 Micscape - the monthly Microscopy Magazine
 URL < http://www.demon.co.uk/micscape/ >      
----------------------------------------------------------------------------

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From: milstone <[email-masked]>
Date: 15 Mar 1996 22:06:27 GMT

>>I have been following this thread with great interest.  Does anyone out
>there know of Intel-based imaging software?
>Thanks,

NIH-Image is apparently now available for the PC somewhere at Zippy.nimh.nih.gov.

--dave

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From: [email-masked](RAYMOND J. WEIMER )
Date: 15 Mar 1996 17:42:00 GMT

Thanks,

Ray

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From: [email-masked] (Greg Remington)
Date: 15 Mar 1996 22:39:54 GMT

>there know of Intel-based imaging software?

If you are interested in >8 bit monchrome camera control, image display,
and image processing, check out my web site:

http://www.gkrcc.com/gkrcc

48 bit color support will be available soon...

Greg

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From: [email-masked] (Sheldon L. Epstein)
Date: 17 Mar 1996 00:07:04 GMT

In article <[email-masked]>,
>there know of Intel-based imaging software?

Sure do Ray.  I purchased mine at Epix, Inc. at 

			[email-masked]
			847:465-1818  - Suburban Chicago
			       -1919  - FAX

			Shel Epstein, [email-masked]

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From: [email-masked] (Tom Stephenson)
Date: 17 Mar 1996 04:03:13 GMT

K. D. Ham ([email-masked]) wrote:
: SG <[email-masked]> wrote:
: >
: >I would be grateful for help from somebody who has experience of 
: >making computer images of microscopic objects using a digitising camera 
: >directly attached to a light microscope (and thereby avoiding the need in 
: >making conventional photographs). 
: >
: >I have got some manufacturer's prospectuses about CCD cameras for microscopes
: >but I would like to hear from the people who actually use those cameras 
: >whether it is possible (and practical!) to use this way for making images of 
: >biological preparations (cells and tissues) with "publication" quality.
: >
: >Sergei Gutnikov, D.Phil.
: >Department of Experimental Psychology
: >Oxford University
: >UK                                          [email-masked]
: >
: >
: >
: >

: If you already have a normal video camera that is attached to a microscope, you may 
: want to check out a frame grabber from Play Inc. (www.play.com) I think it is called 
: Snappy and costs less than $200US. I haven't used it, but you can download a demo 
: program that demonstrates picture quality (impressive on screen). By some 
: proprietary algorithm, they claim to be able to far exceed the TV resolution you 
: expect from such a camera. By printing those images, it should be possible to 
: evaluate whether they would be publication quality. I believe they support both PAL 
: and NTSC video sources.

I bought one of the "Snappy" modules for my son. He's a computer nerd and a video
buff too. He hooked the snappy module up to his pentium and showed me how he could
frame grab from his VCR, Camcorder, etc. The pictures were really impressive.

You can take multiple frames (as in movies) but you can't keep up with 30 frames/
second unless you have a REALLY fast machine.

Tom S.

PS: FWIW, I have a camera on my workstation (SGI Indy) and can take pictures
or movies with it. The camera was really designed for video conference and
doesn't really lend itself to attach to a microscope. My Indy does have video
in features that can record SVGA from some external source.

: I hope this helps.

: Kenneth

--
'You can't roller skate in a Buffalo herd, but you can be happy if you've
a mind to - ' Roger Miller

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From: [email-masked] (J.Hearns)
Date: 18 Mar 1996 10:30:24 -0000

Hi Sergei.
Some suggestions:

A) you could contact Professor McGee who runs the Oxford Telepathology 
   Centre. I've been trying to get in contact with him myself. I sent
   a fax to the telepathology centre on 23 Feb. If anyone there is 
   listening in, I'd appreciate a reply :-)

B) I'm working on telepathology. I recently went to the IPOT 96 conference
   in Birmingham, and saw some nice CCD cameras like you describe.
   
As far as I can see things, there are 3 main ways of doing this

1) use a conventional video camera plus frame grabber. We have a PC,
   plus a frame grabber. I'll be happy to give you more details.
   The quality of this approach is obviously dependent on the particular
   camera you have on the microscope. We have a single-CCD JVC camera
   at the moment.
   Software can then save the images in popular graphics formats.

2) use a high quality 'still' CCD scanning camera. I saw threee nice
   models at IPOT. The Sony one comes to mind. Good quality, to
   my eye.

3) We are also looking into using video codecs for direct transmission
   of video from the microscopes. I have two 'Cellstack' boxes
   on loan from K-Net (http://www.k-net.co.uk). These boxes allow 
   both transmission and reception of PAL (or NTSC) video and DAT qaulity
   stereo sound on an ATM network. They seem to perform very well, though
   I've only just received them. I'll be happy to tell anyone about our
   progress. Though, these boxes probably won't suit Sergei.

Please drop me an email if I can help further.

Dr. John Hearns
AMInet Project
Guys and St. Thomas' Hospitals
[email-masked]

-- 
================================================================
| Dr. John Hearns : Guy's and St. Thomas' Hospitals, London    |
| email : [email-masked]  Tel: +44 171 922 8072           |
| www   : http://www-ipg.umds.ac.uk/~johnh/                    |

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From: [email-masked] (Ard Jonker)
Date: Tue, 19 Mar 1996 11:17:19 +0100

>>>and manipulation you can do with this program are truly amazing! I'm

You could also try NIH-Image, a free image processing package from 
zippy.nimh.nih.gov in the /pub/image directory.
It supports AV and PPC (X500 series) frame grabbing directly.

Ard
PS. Seems to run on a PC using Executer (-tor) from Ardi (not to be mistaken for
Ard!)

-- 
Ard Jonker                                     |Meibergdreef 15
Dept of Anatomy & Embryology       |1105 AZ Amsterdam
Dept of Histology and Cell Biology    |The Netherlands
Faculty of Medicine                         |tel +31 20 566 5396
University of Amsterdam                [email-masked]

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From: [email-masked] (Jack Sanders)
Date: Wed, 20 Mar 1996 17:38:17 GMT

>UK                                          [email-masked]

What types of micrographs will you make?

1.	Color? (effects the memory requirements, processor speed, and
software choice)

2.	Low light levels? (image intensification may be required)

3.	Wavelength sensitivity? (do you need something for all
visible, some visible, and do you want to filter out IR or some
visible)

4.	Depth of focus? (flat fields are easy, unless contaminants can
effect the features you are interested in; if the item is not flat,
you need to consider the objective optic depth of focus)

5.	Magnification? (one of the great things about this method is
that you get a built-in magnification equal to the change in pixel
size.  On one project I worked on, the CCD pixel was 6.7 micrometers
long, while the monitor pixel was 330 micrometers long; 50x for the
choice of the right monitor!  I then only needed a 4x objective to
obtain the 200x required.)

6.	Light source? (transmission, reflection, and if reflective, do
you need oblique lighting)

7.	Money?  (how much do you want and need to spend?  can you
scrounge some equipment?  often, there are microscopes, computers,
monitors, and even cameras around the lab(s).  save your money for
memory, preocessor speed, memory, software, memory, and a really great
camera)

My application was particle counting and morphology.  I used a Mac
IIcx with 16Mb of DRAM, 70Mb hard disk, a very high resolution Kodak
Megaplus CCD camera (1.4 million pixels: _WOW_), NIH Image software,
and a Perceptics frame grabber designed just for the Kodak camera.
Collecting frames was kind of slow, and manipulating images was
_incredibly_ slow.  I would suggest a powerPC or Pentium system,
especially for HiRes or color work.  Image is great, and only costs
the time to download it.  The last time I looked, it was only for the
Mac (powerPC included).

Jack Sanders

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From: [email-masked] (Jud Ready)
Date: 21 Mar 1996 00:11:36 -0500

>>biological preparations (cells and tissues) with "publication" quality.

[For British Lb. Sterling convert $ amounts using published exchange rates]

A CCD camera costs what?, $6k for it and some of the gear.  I'd take my money,
keep taking the micrographs, and buy a *nice* scanner.  HP and other
manufacturers are upto about 1200 dpi now which is plenty high for
publications. Scanners are $600-$1k. You get nice software to manipulate
your images, plus text recognition software that links directly to a word
processor.  Lotsa other uses too.  

I have a $50k CCD boroscope that I've used maybe three times.  I use my
$600 scanner almost every single day.

   - Jud Ready				;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
					;; Georgia Institute of Technology ;; 
  [email-masked]		;;---------------------------------;;
					;;     	     School of		   ;; 
______________________________________	;; Materials Science & Engineering ;;
| My recently renovated home page:    |	;;	 	 &		   ;;
| http://www.prism.gatech.edu/~wr35/  |	;;  The Packaging Research Center  ;;
|_____________________________________|	;;        Atlanta, Georgia	   ;;
					;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

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From: Anatoly Portnoy <[email-masked]>
Date: 26 Mar 1996 21:37:09 GMT

Hi there,
I have just what you are looking for - fully automated image aquisition/analysis system. Please 
call me at USA - 303-978-5335. We'll see how we can help to solve your problem.
Thanks,
Anatoly Portnoy

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From: [email-masked] (Una Smith)
Date: 29 Mar 1996 00:31:49 GMT

In my department, a few lab groups have digital camera attachments
on their microscopes, but this represents a huge investment in stuff
that isn't used all that often.  By far the most practical setup is
to have a conventional camera mount on the microscope, and a scanner.
Most of us shoot slide film, and either send the exposed film to a
commercial shop for digitizing, or scan in the developed slides as
needed.

This system works equally well for microscopy and for photography of
whole specimens and field localities, so you get more for your money.

I prefer to shoot all primary micrographs on color slide film (good
for giving talks, and archiving and viewing data).  I use a slide
scanner to make digital images that can be manipulated into plates
for publication.  My only hesitation is that I don't know if color
slide images that are scanned in, then converted to grey-scale, are
as good as B&W negatives that are scanned in.  Note, the hardware
used is the same regardless;  this is strictly a question of which
film is better for recording grey-scale details, and whether the
software (Adobe Photoshop, in my case) does a good job of swapping
color maps.

Does anyone here have a strong preference for using B&W negatives
over color slides, when the output is a grey-scale digital image?

Thanks,

	Una Smith

NOTE:  I've set followups to the group where this topic belongs,
sci.techniques.microscopy.