[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? 

Thanks,
Jerry Cooper


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

It is the Helicon site I was looking for.

Thanks

John

>  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
one
>that I use (again, for microscope images) is Helicon Focus
>http://www.heliconsoft.com/heliconfocus.html 
>
>Here is my original reply, that may also be of interest:
>
>Dear John,
>
>Might this be the Photosynth project being developed by Microsoft?
>
>See:
>http://labs.live.com/photosynth/ 
>
>and a presentation given at TED
>http://www.ted.com/index.php/talks/view/id/129 
>
>Regards,
>
>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:
>www.nhm.ac.uk/naturenavigator/ 
>
>-----Original Message-----
>From: taxacom-bounces at mailman.nhm.ku.edu 
>[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Richard
Zander
>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
sections,
>then combined the lot into an animated GIF, supposing that fast
flipping
>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,
I
>>  am asking anyway.  Please forgive my request.
>>
>>  The poster listed a software company that had a relatively
inexpensive
>
>>  program that allowed combining multiple photos of the same object
into
>
>>  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
the
>>  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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>
>_______________________________________________
>Taxacom mailing list
>Taxacom at mailman.nhm.ku.edu 
>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 


-- 
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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