[Taxacom] increasing depth of focus & 3D images

Jerry Cooper cooperj at landcareresearch.co.nz
Mon Aug 6 15:13:01 CDT 2007

This post triggered  a related question.

The software packages which increase depth of focus - such as Helicon,
CombineZ and Automontage - all use a stack of images taken at different
focal planes through the object. It must be possible to use this same
stack to create a pseudo-3D composite image that can be rotated in 3D to
some extent. From superficial digging I think the image analysis folks
even have a name for the technique - 'shape from focus'. However, I
can't find any software that actually does it. Photosynth is a very cool
piece of software but not quite what I'm after. Our image slices are
generated against a known frame of reference using a stepper motor
moving the focal plane. That extra information must surely make the task
simpler and more precise.
So, does anybody know of any software that does this? 

Jerry Cooper

>>> John La Duke <john_laduke at und.nodak.edu> 7/08/2007 4:10 a.m. >>>

It is the Helicon site I was looking for.



>  I just replied to John off-list and now, reading Richard's
>contribution, I realise that I had got hold of the wrong end of the
>stick (so to speak).
>There are several software products that cope with image stacks. The
>that I use (again, for microscope images) is Helicon Focus
>Here is my original reply, that may also be of interest:
>Dear John,
>Might this be the Photosynth project being developed by Microsoft?
>and a presentation given at TED
>Charles Hussey,
>Science Data Co-ordinator,
>Data and Digital Systems Team,
>Library and Information Services,
>Natural History Museum,
>Cromwell Road,
>London SW7 5BD
>United Kingdom
>Tel. +44 (0)207 942 5213
>Fax. +44 (0)207 942 5559
>e-mail c.hussey at nhm.ac.uk 
>Species Dictionary project: www.nhm.ac.uk/nbn/ Nature Navigator:
>-----Original Message-----
>From: taxacom-bounces at mailman.nhm.ku.edu 
>[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard
>Sent: 06 August 2007 16:26
>To: john_laduke at und.nodak.edu; taxacom at mailman.nhm.ku.edu 
>Subject: Re: [Taxacom] images
>I remember the exchange but not the company.
>I tried photographing a microscopic item at different optical
>then combined the lot into an animated GIF, supposing that fast
>would artificially deepen the optical section and make a kind of 3D
>image in the brain. Didn't work, but might be my brain's fault. Good
>luck with this and I hope it works somehow.
>Richard H. Zander
>Voice: 314-577-0276
>Missouri Botanical Garden
>PO Box 299
>St. Louis, MO 63166-0299 USA
>richard.zander at mobot.org 
>Web sites: http://www.mobot.org/plantscience/resbot/
>and http://www.mobot.org/plantscience/bfna/bfnamenu.htm 
>For FedEx and UPS use:
>Missouri Botanical Garden
>4344 Shaw Blvd.
>St. Louis, MO 63110
>>  -----Original Message-----
>>  From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
>>  bounces at mailman.nhm.ku.edu] On Behalf Of john_laduke at und.nodak.edu

>>  Sent: Monday, August 06, 2007 10:04 AM
>>  To: taxacom at mailman.nhm.ku.edu 
>>  Subject: [Taxacom] images
>>  One of the lists I am on sent out a post in the last six months
that I
>>  cannot relocate.  Although this list is not the most likely choice,
>>  am asking anyway.  Please forgive my request.
>>  The poster listed a software company that had a relatively
>>  program that allowed combining multiple photos of the same object
>>  one image.  It effectively allowed you to take multiple shots at
>>  vastly different focal points and then put all of
>>  them into a single image.   The reference to this company was not
>>  main focus of the post but was almost an aside.
>>  Ring any bells???
>>  John
>>  --
>>  John La Duke
>>  Associate Dean of Arts and Sciences
>>  University of North Dakota
>>  Grand Forks, ND 58202
>>  701 777 3641
>>  _______________________________________________
>>  Taxacom mailing list
>>  Taxacom at mailman.nhm.ku.edu 
>>  http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu 
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John La Duke
Dept Biology, Box 9019
University of North Dakota
Grand Forks, ND 58202

  please no voice mail as I do not check it often
701 777 4678 office Biology
701 777 2621  dept

The inertia of custom must be overcome - Marshall Sundberg, Amer. Sci
63: 307

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