MacIntosh Video RFLP Digitizing Analysis

Andrew F. Cockburn afc at gnv.ifas.ufl.edu
Thu Oct 24 11:20:29 EST 1991


In article <9110230157.AA26288 at ccvr1.cc.ncsu.edu>, nmodena at unity.ncsu.edu writes:
> 
>                                 October 22, 1991
> 
> Looking for advice from the Network:
> 
> Re: RFLP Video-imaging Setup and Use
> 
> We have ordered:
>         MacIntosh FX computer 
>                 16 Mb RAM
>                 160 Mb Hard Drive
>         Optical Drive for Mass Storage
>         19" Sony Trinitron Monitor
>         JVC TKH70 Still Image Video Camera
>         RasterOps 24XLTV Quick Capture Card
> 
> Our purpose is to capture, store and transmit RFLP radiographs
> for analysis here and in other labs working, in particular, on
> Maize Genome Mapping and Genetic Analysis (but not restricted to
> maize knowledge only).
> 
> Looking for suggestions and experiences using this equipment and
> similar in electrophoretic gel analysis.
> 
> Hints and kinks welcome!
> 
> Data storage, retrival, compression and transmission wisdom.
> 
> FTP sites with FAQs, appropriate software, etc.
> 
> And anything else I forgot to mention that you think it is worth 
> knowing about.
> 
> On behalf of:   Paul Sisco
>                 Crop Science Department
>                 1250 Williams Hall
>                 North Carolina State University
>                 Raleigh, NC  27695-7620        
>                 tel. (919) 515-2704
> 
> E-mail responses to:
> 
> 
> +------------------------------------------------------------------+
> |     In person:  Steve Modena     AB4EL                           |
> |     On phone:   (919) 515-5328                                   |
> |     At e-mail:  nmodena at unity.ncsu.edu                           | 
> |     By snail:   Crop Sci Dept, Box 7620, NCSU, Raleigh, NC 27695 |
> +------------------------------------------------------------------+
>          Lighten UP!  It's just a computer doing that to you.
> OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
I have been looking at hardware/software to analyze RFLP gels.  We
narrowed our choices to software running on Sun workstations.  The
two systems we compared are made by Millipore (BioImage) and pdi.
We have ordered a BioImage system.

Our reason for going to a workstation was that the image files produced
by scanning an autoradiogram are several MB each.  An ordinary PC
(even a 486) is just not going to be able to display and manipulate
these very fast.  I presume the same to be true of a Mac?  In a few
years most of us will be using phosphor imaging instead of film to 
record autorads, and the files will increase in size by another order of
magnitude (8 logs of dynamic range!).

The two systems I mentioned use proprietary image analysis software
to locate bands and lanes automatically, calculate migration distances
and MWs automatically, and do fragment pattern matching.  This can
all be dumped into your database au jour.  I don't know if equivalent
software is available for other platforms.  We are definitely looking
forward to retiring our rulers and Lotus size calculation macros.

Finally, all of the systems and devices that I looked at can read and
write TIFF files.  As long as your system has this ability, you should         
be able to exchange data with other labs, even those with different 
platforms.

Disclaimer: I have no association with any company mentioned, and 
mention of any product does not constitute endorsement.
 
#################################################################
#Andrew F. Cockburn                        # Any opinions       #
#Medical and Veterinary Research Laboratory# expressed are not  #
#Agricultural Research Service, USDA       # those of the       #
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#INTERNET: AFC at gnv.ifas.ufl.edu            # government         #
#PHONE: 904-374-5873                       #                    #
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