LONG - PHosporImager - compilation of replies

Jonathan B. Marder MARDER at agri.huji.ac.il
Thu Aug 19 21:13:05 EST 1993


WARNING - THIS IS RATHER LONG
I did some VERY limited editing - forgive me for not having the time to cut it
down to size!

These are the replies I received on the PhosphorImager systems available.
As a potential customer, I found these replies extremely valuable.  Thanks
very much to all who contributed.  I may get to check out a couple of systems
soon and will add my own comments at a later date.


From: OKADA Yasushi <mm37301 at secc.ecc.u-tokyo.ac.jp>
Return-Path: <mm37301 at secc.ecc.u-tokyo.ac.jp>
Message-Id: <9308160408.AA26736 at ecc-s4.ecc.u-tokyo.ac.jp>

>1.  Which system do you use?
Fuji BAS-2000.

>2.  Which isotopes do you detect?
32P, 125I, 35S

>3.  Do you use the system for detecting luminescence (Biorad option)?
No.

>4.  What is the host computer and operating system?
SUN, UNIX.

>5.  Do you (or can you) login to the host from a remote terminal?
Yes.

>6.  Can you download the data to a remote computer?
Yes.

>7.  Do you have the data-analysis programs loaded on a remote computer?
>    If so, did you need to buy extra copies of the software?
Yes.
Yes, of course.

>8.  Do you have the programs on a network server (e.g. Novell) and then run
>    them on a remote computer? Did you need a special software license?
No.

>9.  How would you rate the software for handling the images i.e. annotations,
>    adjusting contrast, other manipulations?  Can you easily process the
>    images into various standard formats e.g. GIF, JPEG, etc.?  Do you use
>    additional (e.g.) public-domain software as well, instead?
It is quite easy to handle the image.  We routinely use contrast adjustment,
annotation and quantification.  We have not tried data-transfer via other
standard formats, because the software works quite well and we do not find
the need to do so.

>10. Can you easily incorporate images and/or data into documents (e.g.
>    under MacIntosh or MS-Windows environment.
It is possible, but not an easy task to transfer the data/ image into
Mac or MS-Windows.

>11. How do you produce hard copies of the images, and are they "publication
>    quality?
We use Fuji Pictrography.  The quality of its output is publication quality.


>12. How would you rate the data analysis software (i.e.
>    quantification)?    Can you easily move the raw or processed data into
>    Lotus, Excel or similar?
Quantification is quite easy, and the software is self-contained.  In some
case, we transfer the quantification result into DOS-based spread sheet
software via text data.

>
>I would appreciate also any other impressions, comments that you may think
>relevent.
Although we use BAS2000, a UNIX based system, Fuji supplies Mac Based BAS1000
also.  If you consider the ability to data transfer between Mac, it may work
well.

Hope this helps.

Yasushi Okada
Department of Anatomy & Cell Biology
University of Tokyo
JAPAN
Email:mm37301 at secc.ecc.u-tokyo.ac.jp
Fax:81-3-5689-4856

==========================================================================
=========
From: levenson at cs.duke.edu (Richard Levenson)
Message-Id: <9308162105.AA10832 at juliet.cs.duke.edu>

Greetings:

We are satisfied owners of Molec Dynam PhosphorImagers here at Duke.

2.  35S, 32P, 125I are routinely imaged.

3.  No luminescence.

4.  Host computer is Compaq 486/Windows 3.1, networked via PCNFS to a SUN
workstation.

5.  ALthough instructed not to, we have successfully scanned images directly
to the SUN via PC-NFS without evident problems.  As SUN files, these would
be accessible remotely.  Image analysis across the net should not involve
much transfer of files themselves, since 5 megs can slow things down.

6.  But downloading is not a problem if the net is not easily overwhelmed, I

reckon.  Transfer of files on disk is a problem unless you have removable
media of some sort other than floppies.  The Mol. Dynam comes with a tape
backup installed but it's too slow to be useful for file transport.

7. The file analysis software is ImageQUANT which comes on floppies and is
not copy-protected.  There seems to be no reason why remote analysis on a PC
should be a problem provided it's networked to the host in some way.

8.  No experience with running programs across a net.

9.  The software is reasonable good (for PC-based stuff) for image analysis.
THe automatic box or region numbering is inflexible in it's default mode and
there seem to be a few bugs in the recent release in terms of handling on
screen annotation.  The software allows one to export in standard TIFF
format with 8 or 16 bit depth and these files can be analyzed with NIH Image
or any other package you would like.

10.  Images can be easily incorporated into docs by doing a screen-grab,
saving the files as Windows bitmap images.  These will go right into
Powerpoint or other Windows software for slides or prints. In TIFF format,
they can be Macintoshized for image handling in Photoshop or other packages.

11. The newer printer driver works with a standard Laserjet 4 printer and
produces pretty good images (for many purposes I would say it was
publication quality).  Screen-grab and export to Powerpoint produces truly
P.Q. slides or negatives or they can be printed directly with a color
printer.  The Imagequant software can print directly to a color printer
(3-10,000 dollars) as well.  Printing is pretty slow with the current driver
and the Laserjet (several minutes/print), but not totally unacceptably.
However, it doesn't release the computer, so you have to wait until it's
done.

12.  Quantitation is good, and overall, the system is extremely accurate.
Truly linear over 5 logs (tested on our machine).  Very reproducible and
trustworthy.  The data is easily exported to EXCEL or other spreadsheets
(simple cut and paste or automatically).

13.  We like it.  It's not perfect and there may be better software
packages, but overall, it's usable and sensitive and accurate.  You can
transfer the files via ethernet to any other computer host (Mac, SUN, SGI,
other 486's) so you are not limited to the software it comes with.

Good luck.

richard

==========================================================================
=====

From: greg at mendel.llnl.gov
Message-Id: <9308161602.AA07215 at mendel.llnl.gov.>
Reply-To: Greg Lennon <greg at mendel.llnl.gov>


Although I don't have the time to answer in detail your questions,
I would definitely recommend you go for the Molecular Dynamics
phosphorimager.  We have one, and have tried the Biorad one  ****SEE ADDENDUM***
Our MD PI is networked via Ethernet, so we have quite a bit
of archival storage capacity as well (with an optical jukebox.)
The MD software is good, and the hardware is reliable - it's your
best choice.  I do not know about service in your area, but in
ours it is good.

Greg Lennon
Lawrence Livermore National Lab
Livermore, CA 94550


ADDENDUM ***************
The cassette system used by Biorad was very awkward to use;
the chemiluminescent ability was nonexistent at least in our
hands; the software was error prone; the machine couldn't even
accurately and reliably see our radioactive markers. Perhaps
we had an early machine that was released too early, but in
any case it's performance was abysmal.

Greg Lennon
greg at mendel.llnl.gov

==========================================================================
=========From ???@??? Wed Aug 18 08:39:01 1993

Message-Id: <9308172235.AA05541 at jupiter.genetics.bio-rad.com>
To: marder at agri.huji.ac.il
From: dpatters at jupiter.genetics.bio-rad.com (Doug Patterson)
Subject: Phosphor Imaging Systems


Dear Dr. Marder,

I am writing in response to your request for more information regarding
Bio-Rad's Model GS-250 Molecular Imager, phosphor imaging system:

  1) Bio-Rad Model GS-250 Molecular Imager

  2) We can currently detect basically all isotopes except tritium. We will
have a special phosphor screen for tritium in the immediate future.

  3) As you noted, the Bio-Rad system is the only system capable of
chemiluminescent detection in addition to ionizing radiation.

  4) We offer software for both Windows (DOS 5.0or >) and Macintosh (System
7+) platforms.

  5) The only way to remotely control the Imager would be to control the
host computer by using software such as Timbuktu (Macintosh), or Carbon
Copy (Windows).  The scanner is controlled and sends the information via a
SCSI interface.

  6) The image files can be send to remote computers via any standard
network (Ethernet).

  7) We offer site licenses for using the software on additional stations.

  8) We do not have a server version.

  9) We are the only company offering Macintosh software.
[N.B. I was told by our local agent that FUJI do/will also offer Mac software - JM]
Our Windows software offers more features than any other Windows package.
The images can be saved in 8 or 16 bit TIFF format for exportation to other
analysis and publication programs.

  10) Incorporating images into other documents is easy using the TIFF
format or a screen capture program.  Adobe Photoshop is the best program
for image annotation and manipulation.

  11) For hard copy since with Phosphor Imaging systems you eliminate film,
we have recommend the following:


   For documation: PC- HP LaserJet 4 with an XLI 256 gray scale card installed.
                   Mac- HP LaserJet 4M or LaserWriter PRO 630

   For Publication: 1) Send TIFF file on disk to publisher
                    2) Output image to slide maker
                    3) Output image to photographic quality digital dye sub
      printer.

   12) All data in the software's results table can be exported to programs
such as Excel using the clipboard.

I am the product manager for this system and would be happy to provide you
with any additional information you may need. We also have a local
distributor: Eisenberg Bros. Ltd. 972-3-697-9876.

Thank you for considering Bio-Rad for your image analysis needs.

==========================================================================
=========

From: jow at helix.nih.gov (Jim Owens)
X-Sender: jow at 128.231.128.13
Subject: Re: Phosphor Imager information needed

In article <MARDER.14.0010F139 at agri.huji.ac.il>, you write:
>
>1.  Which system do you use?
Molecular Dynamics.  We got it about a month ago.
>2.  Which isotopes do you detect?
P-32 and S-35
>3.  Do you use the system for detecting luminescence (Biorad option)?
No, I think BioRad is the only one that claims to do that.
>4.  What is the host computer and operating system?
Molecular Dynamics now puts together their own generic '386 with Windows
and their proprietary software (ImageQuant) loaded.  They will include
Ethernet and SCSI interfaces at your request.  Be sure to specify the type
of ethernet wiring (thick, thin or 10BaseT).  We didn't and got thin
ethernet connectors.
>5.  Do you (or can you) login to the host from a remote terminal?
We don't and do not intend to make it a server for others.
>6.  Can you download the data to a remote computer?
Not yet since it has not been hooked up to our local ethernet, but we plan
to do this.
>7.  Do you have the data-analysis programs loaded on a remote computer?
Yes
>    If so, did you need to buy extra copies of the software?
Legally, yes, but we were told by the sales reps that Molecular Dynamics
would not worry about it.  Afterall, we had already spent $55 000.
>8.  Do you have the programs on a network server (e.g. Novell) and then run
>    them on a remote computer?
No, we hadn't thought of that.
>Did you need a special software license?
I don't know.
>9.  How would you rate the software for handling the images i.e. annotations,
>    adjusting contrast, other manipulations?
We had demonstrations of the BioRad and Molecular Dynamics machines, and I
found the Mol. Dynamics software easier to use.  It just may be that a) I
had used someone else's Mol. Dynamics densitometer which uses the same
software, and b) the Mol. Dynamics' software has had much more development.
 The software we got was a later version than the one I had used on the
densitometer and seems more intuitive.
>Can you easily process the images into various standard formats e.g.
>    GIF, JPEG, etc.?
I think so, but have not tried it yet.
>    Do you use additional (e.g.) public-domain software as well, instead?
I have transfered the .gel (image) files to a Macintosh via Apple File
Exchange and accessed them by "import"ing into NIH Image.  So far, I have
not done anything but print the image on a LaserWriterIIf.
>10. Can you easily incorporate images and/or data into documents (e.g.
>    under MacIntosh or MS-Windows environment.
Relatively easily.  Data can be imported in Excel.  Molecular Dynamics did
not include Excel for Windows; they felt it would be cheaper for us to buy
it ourselves than from them.
>11. How do you produce hard copies of the images, and are they "publication
>    quality?
So far, just LWIIf.  That is NOT publication quality.  Mol. Dynamics' sales
reps claimed that a LaserJet4M would give nearly publication quality.  They
found the best printouts were on dye-sublimation color PostScript printers
($9000 to $20000(US), OUCH!)
>12. How would you rate the data analysis software (i.e. quantification)?
Molecular Dynamics does not include any data analysis ability in their
software.  They prefer not to do anything more than generate data, and let
you manipulate it on spreadsheet or graphing software.  They want you to
understand what you are doing when you analyse the data.  It is easy to
move the data to other programs, like Excel.
>    Can you easily move the raw or processed data into
>    Lotus, Excel or similar?

The sales reps told us that their company is working on a Macintosh version
of the software.  My guess is that they will use Image for the image
processing and enhancing.

So far we have one user who is just using it to test radioactive
immuno-reagents on microscopic slides.  If they look OK after overnight
exposure, he then goes on to the 5 or 6 day exposures on photoemulsions for
in situ localization in photomicrographs.  If they are not exposed enough
overnight on the PhosphorImager, he says they will not work with the
emulsion.  So he can save a week's work if the reagents are not good.

Good luck,

Jim Owens

==========================================================================
========
Date: Wed, 18 Aug 93 00:23:37 EDT
From: Jay Hirsh <jh6u at virginia.edu>
Subject: phosphoimager nightmare

We thought we would pass on information regarding an unfortunate incident
we've gotten ourselves into in trying to purchase a phosphoimager.  We hope
our experience will be a lesson to aid others in preventing this sort of
occurrence.

The story starts last year when we decided to purchase a phosphoimager.  Our
decision basically came down to two instruments, one about to be released
instrument, and one established instrument from Molecular Dynamics.  We had
heard good things about the MD instrument, but from the other company we
could get a workstation based gel reader thrown in for the price of an MD
phosphoimager alone.  The catch was that the new instrument wasn't available
for an on site demo- we could try the instrument at the factory, but
couldn't get one here to play with.

So, one of us (SK) stopped by the factory, and spent an afternoon playing
with both the phosphoimager and the sequence gel reader.  He was fairly well
impressed, although the instrument wasn't yet up to par on all fronts.  We
were assured that these deficiences would all be corrected by the time of
shipment,  and to protect us, they would provide a 30 day money back
guarantee.  In the words of a fax addressed to me from the product manager
in May 1992, "If you or your Colleagues are not completely satisfied with
the system once it is installed, we will issue a full refund."

So, we went ahead with the purchase, with the company and a UVA purchasing
agent signing onto a bid form which included the statement "Shall include a
30 day full money back return warranty".

On arrival of the phosphoimager, we were unhappy with the instrument for a
number of reasons.  The field engineers were not able to get the instrument
running off a PC that met the specifications they gave us.  It's still
connected to their PC, not ours.  Although capability to run off a Mac is
advertised, they were similarly not able to run all functions of the machine
from a Mac.  Additionally, the first imager shipped was defective in a
number of other respects, and was replaced within two weeks of its
installation.

With a functional phosphoimager finally running, we proceded to run some
tests with a 14C resolution/sensitivity standard provided by the
manufacturer.   Our tests show that the installed instrument was inferior to
an MD instrument in our chemistry department in image quality, resolution,
and sensitivity.  In addition, scanning time is roughly 7 fold slower than
on the MD.  To be fair, our installed phosphoimager lacks the horizontal
"flaring" apparent on the MD, and it will image chemiluminescence, which the
MD won't.  However, the chemiluminescent imaging is slower than film.  The
manufacturer's representatives tell me that they have data that contradicts
ours, i.e., that their instrument is superior to the MD in the terms of
sensitivity.  However, we have not seen that data, and we can only procede
on what we have seen directly.

Within days of getting and testing the functional instrument we decided that
we were sufficiently unhappy to request a full refund.  Then the fun
started.  We were told by the manufacturers chief legal counsel that "full
money back warranty" does not mean what we had supposed!  It means, in his
interpretation, a warranty to perform up to THEIR specifications, not to OUR
satisfaction!  He further told one of us (JH), in a phone conversation, that
he wasn't concerned that we weren't happy with the instrument.  His only
concern was the signed contract.  He did offer to take the instrument back,
for a $40K "restocking" fee to cover their expenses.  Needless to say, we
declined this offer.  What ever happened to companies concerned with
customer satisfaction? We are absolutely flabbergasted by this behavior, and
can't understand why they are trying to stick us with a piece of equipment
that we don't want!

The complication with all this is that during the lengthy installation
process, partial payment was made to the company.  As things now stand, the
company is sitting on a fair chunk of our money, and we have turned all his
over to our own legal staff.  A vendor complaint form has been filed against
the company, which if successful, would prevent it from future sales to the
state of Virginia.  We have a phosphoimager that we would rather not have,
and all this has wasted an enormous amount of time and energy.

Some lessons from the above:

1)  In making a large purchasing agreement, make sure that legal staff check
over the detailed wording of the paperwork.  Also, make sure that you get a
copy of the final paperwork before it gets signed, just to make absolutely
sure that it says what you expect it to say.

2)  If there is a money back warranty, make sure that payment is not made
until you are satisfied.  In our case, it would have been possible to build
in an inspection clause, such that payment wouldn't have been made until we
signed off.

3)  Never put any faith whatsoever in oral agreements made by company
representatives.  Everything must be in writing.  Furthermore, don't put any
faith in advertised claims of phosphoimagers or other instruments.  Insist
on a lengthy on-site trial period for adequate evaluation.


We hope this recounting will prevent similar occurrences elsewhere.


Jay Hirsh  (jh6u at virginia.edu)
Steve Kay  (sak5y at virginia.edu)
University of Virginia, Dept Biology

==========================================================================



From: djackson at pennsy.med.jhu.edu (Donald Jackson)
Message-Id: <9308181226.AA03842 at pennsy.med.jhu.edu>

>1.  Which system do you use?

We have a Molecular Dynamics machine which is universally hated and cursed throu
ghout the building.  (just so you know how I feel ;-))

>2.  Which isotopes do you detect?

Mostly S-35 and P-32

>3.  Do you use the system for detecting luminescence (Biorad option)?
No

>4.  What is the host computer and operating system?

The machine is run by a 386sx PC (compaq?) using a Windows-compatible software p
ackage.  We have found this to be unwieldy and buggy.  I believe the machine cou
ld be networked for other PC's but ours is not.

>5.  Do you (or can you) login to the host from a remote terminal?

No (see above).

>6.  Can you download the data to a remote computer?

Yes-by moving it onto floppies or syquest cartirdges.  I should probably mention
 that our department is otherwise Mac-based, which is why this machine is orphan
ed without network connections, etc.

>7.  Do you have the data-analysis programs loaded on a remote computer?
>    If so, did you need to buy extra copies of the software?

We do our analysis using excel or some such on other machines.

>8.  Do you have the programs on a network server (e.g. Novell) and then run
>    them on a remote computer? Did you need a special software license?

No-as I said, the machine is the only PC around.

>9.  How would you rate the software for handling the images i.e. annotations,
>    adjusting contrast, other manipulations?  Can you easily process the
>    images into various standard formats e.g. GIF, JPEG, etc.?  Do you use
>    additional (e.g.) public-domain software as well, instead?

I don't know of anyone who has used the machine for image capture.  We mostly us
e it for quantitation.  It is possible to capture an image, I think as a TIFF
file or some such and manipulate it on a Mac.

>10. Can you easily incorporate images and/or data into documents (e.g.
>    under MacIntosh or MS-Windows environment.
>11. How do you produce hard copies of the images, and are they "publication
>    quality?

We're still in the dark ages here... just using our computers to crunch numbers
and type papers on.  I've been trying to persuade people we needa serious graphi
cs machine (image capture, 24 bit, hi quality color printer, etc.) so we
can do our own graphics, but I haven't convinced anyone with $$.  Hard
copies are produced with X-ray film.  The imager has a laser printer hooked up,
but it's pretty worthless.

>12. How would you rate the data analysis software (i.e.
>    quantification)?    Can you easily move the raw or processed data into
>    Lotus, Excel or similar?

Actually, that's not too bad. Data can be saved as sylk files to 3.5" disks
and moved to macs, opened w/ most spreadsheets, etcetera.
>
>I would appreciate also any other impressions, comments that you may think
>relevent.

Did I mention how slow the machine is?  Scanning in and displaying a
sequencing gel can take 30 minutes.  Maybe the new machines (this one's a few ye
ars old) have better computers; I'd say this needs a real screamer of a
chip.  I'll freely admit to being biased against windows PC's; we've
certainly had lots of trouble with the imaging software.  All in all,
we aren't impressed.


Anyway, have fun shopping!

Don Jackson
djackson at pennsy.med.jhu.edu

==========================================================================
==========
__
Jonathan B. Marder                 '
Department of Agricultural Botany  |     Internet: MARDER at AGRI.HUJI.AC.IL
The Hebrew University of Jerusalem | /\/ Bitnet:   MARDER at HUJIAGRI
Faculty of Agriculture             |/  \ Phone:    (08 or +9728) 481918
P.O.Box 12, Rehovot 76100, ISRAEL  /     Fax:      (08 or +9728) 467763



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