counting worms

Charles Baer cbaer at darkwing.uoregon.edu
Sat Feb 19 14:19:21 EST 2000


Ladies and Gentlemen,

	A few weeks ago I posted the following notice on the wormnet re
digitizing
the counting of worms.  Below are the replies I received.  Many thanks to
all who replied.

-Charlie Baer

>Ladies and Gentlemen,
>
>My colleagues in Mike Lynch's lab have been counting worms (on 60 mm Petri
dishes) manually under a dissecting scope, which is extremely
time-consuming and labor intensive.  There are various image-analysis
systems that are purported to be able to automate such a procedure, and we
are considering purchasing such a system.  We would very much like to hear
from anyone with experience in counting worms with digital image-analysis
systems, especially those of you with recommendations (positive or negative).
>

>X-From_: eugene.leitl at lrz.uni-muenchen.de  Sun Jan 23 20:31:49 2000
>From: Eugene Leitl <eugene.leitl at lrz.uni-muenchen.de>
>Date: Sun, 23 Jan 2000 20:32:36 -0800 (PST)
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>Cc: nobody at net.bio.net
>Subject: counting worms
>Newsgroups: bionet.celegans
>X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid
>
>Charles Baer writes:
> > Ladies and Gentlemen,
> >
> > My colleagues in Mike Lynch's lab have been counting worms (on 60 mm Petri
> > dishes) manually under a dissecting scope, which is extremely
> > time-consuming and labor intensive.  There are various image-analysis
> > systems that are purported to be able to automate such a procedure, and we
> > are considering purchasing such a system.  We would very much like to hear
> > from anyone with experience in counting worms with digital image-analysis
> > systems, especially those of you with recommendations (positive or
negative).
>
>I'm reasonably certain one can tweak http://las1.ninds.nih.gov/index.nih.html
>with an off-shelf flatbed scanner to do the worm counting.
>
>Are the animals anaesthesized/sluggish or fully mobile? Otherwise you
>should check the scanner speed. If insufficient, you might consider
>using a video grabber board.
>

>X-From_: dfitch at zedat.fu-berlin.de  Mon Jan 24 05:56:43 2000
>X-Sender: dfitch at mail.fu-berlin.de (Unverified)
>Date: Mon, 24 Jan 2000 14:56:13 +0100
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>From: "David H. A. Fitch" <dfitch at zedat.fu-berlin.de>
>Subject: Re: counting worms
>
>Hi Charlie,
>PS.  I remember someone searching for an optical method of counting worms
>in the celegans forum earlier.  Perhaps check the archives of the forum on
>the swmed server:
>http://elegans.swmed.edu/
>Also, to make counting easier, you can put plates of worms in the
>refrigerator (8C) for an hour or so before counting.  The worms will stop
>moving, and will stay in those positions for several minutes after removing
>the plates from the fridge.
>David Fitch
>

>X-From_: crankin at neuron3.psych.ubc.ca  Mon Jan 24 09:59:38 2000
>Date: Mon, 24 Jan 2000 09:44:36 -0800
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>From: Cathy Rankin <crankin at neuron3.psych.ubc.ca>
>Subject: Re: counting worms
>
>Do you need to buy a fancy system?  We use NIH Image which we downloaded
>free by FTP from zippy.nimh.nih.govin/pub/nih-image.  Using it you should
>be able to photograph the plate (or use a frame grabber from a video
>image)and digitize the image of the worms and count them.
>
>Catharine Rankin
>

>X-From_: jjthaden at life.uams.edu  Mon Jan 24 10:23:54 2000
>X-Sender: jjthaden at life.uams.edu
>X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32)
>Date: Mon, 24 Jan 2000 11:46:00 -0600
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>From: John Thaden <jjthaden at life.uams.edu>
>Subject: Re: counting worms
>
>Dear Dr. Baer,
>
>Sorry, I don't have experience with automated image counting, but have
>collected quite a file from IP companies that sell relevant equipment and
>software, because I'm interested not only in counting them, but determining
>if they are alive.  Maybe we can compare notes.  If you hear from others
>with experience, would you mind posting a summary to me or wormnews?
>

>X-From_: iino at ims.u-tokyo.ac.jp  Mon Jan 24 17:30:04 2000
>X-Sender: iino at ims.u-tokyo.ac.jp
>X-Mailer: Macintosh Eudora Pro Version 4.0.1J
>Date: Tue, 25 Jan 2000 10:29:54 +0900
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>From: Yuichi Iino <iino at ims.u-tokyo.ac.jp>
>Subject: Re: counting worms
>
>Hi Charlie,
>
>We are assaying chemotaxis and do a lot of counting also. I have been always
>wondering if there is such a counting system as you are considering, but
>nobody I know is doing this. The Argus system by Hamamatsu Photonics carry a
>counting program, but it is too slow. I wonder if NIH Image might be more
>useful.
>If you manage to set up the system, or know anybody already doing this, it
>would be very helpful if you could let me share the information.
>Good luck for your project.
>Best wishes,
>
>Yuichi
>

>X-From_: pek at sanger.ac.uk  Tue Jan 25 08:01:57 2000
>X-Sender: pek at mail.sanger.ac.uk
>Date: Tue, 25 Jan 2000 15:33:10 +0000
>To: cbaer at darkwing.uoregon.edu (Charles Baer)
>From: Patty Kuwabara <pek at sanger.ac.uk>
>Subject: Re: counting worms
>
>
>Dear Charlie,
>
>If you do not need to recover your worms after counting, then it is very
>simple to attach a finely drawn pasteur pipet to an aspirator and vacuum
>your worms as you count. Obviously a low-tech solution, but one that works.
>
>Cheers,
>Patty Kuwabara
>

>X-From_: gregoc at bu.edu  Sat Jan 29 09:26:57 2000
>Date: Sat, 29 Jan 2000 13:44:46 -0400
>From: gregoc <gregoc at bu.edu>
>X-Mailer: Mozilla 4.05 (Macintosh; I; 68K)
>To: Charles Baer <cbaer at darkwing.uoregon.edu>
>Subject: Re: counting worms
>
>I just wanted to make you aware of a company in massachusetts that makes
>high throughput counters/sorters for small multi-cellular organisms, esp. C.
>elegans.
>The company is Union Biometrica, Inc.  The sorter can sort out populations by
>size and place them into 96 well plates (any given number of worms / well).
>It can also perform a straight count and dispense into a tube.  The
machine is
>very
>accurate and quick.  It will scan, count, and sort 100s of worms in seconds.
>
>If you want further info. please contact Len Tibadou, Sales Manager.
>email:  sales at unionbio.com
>phone: 617-547-7703
>
*******************************************************
Charles F. Baer
Ecology and Evolution Program
1210 University of Oregon
Eugene, OR  97403-1210  USA

Phone: 541-346-4697
FAX:   541-346-2364
Email: cbaer at darkwing.uoregon.edu


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