http://confocal-microscopy-list.275.s1.nabble.com/Aligning-large-stacks-tp7581843p7581875.html
and encoding you can expect good accuracy. Some stages are starting to
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on
http://www.imgur.com and include the link in your posting.
> *****
>
> Thanks again to everyone who replied on and off list. We calibrated the
> objectives as Kees recommended and still found some misalignment. We next
> tried the same with stitching turned off and the alignment was perfect.
> Blurring of fine details was a little worse at image borders but not by
> very much. It turns out that the coded stage really is very good at
> maintaining a position when imaging 100+ tiled images repeatedly in a
> large number on z sections.
>
> All the best,
>
>
> TF
>
> Timothy Feinstein, Ph.D. | Confocal Manager
> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> Phone: 616-234-5819 | Email:
[hidden email]
>
>
>
>
>
>
>
> On 4/3/14, 9:36 AM, "phil laissue" <
[hidden email]> wrote:
>
> >*****
> >To join, leave or search the confocal microscopy listserv, go to:
> >
>
http://scanmail.trustwave.com/?c=129&d=3Ou907qXF6gXlgdAfyFZpLpgH38HKJr2HG1> >GkAd6xg&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalmic
> >roscopy
> >Post images on
> >
>
http://scanmail.trustwave.com/?c=129&d=3Ou907qXF6gXlgdAfyFZpLpgH38HKJr2HDh> >Hwg0ulg&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your
> >posting.
> >*****
> >
> >Hi Timothy,
> >
> >like Kees, we're happy with NIS-Elements stitching, overall. Automatic
> >calibration works best with a high-contrast, continuous sample - tissue
> >sections (even just HE) work fine, e.g. dog ileum (but not, say, breast
> >tissue). Stitching overlap between 5-15% is fine. I did run into problems
> >with too large samples though. A coral I took was ~5k images
> >(x14*y4*z30*ch3), resulting in around a 5GB nd2 file. NIS-Elements
> >subsequently crashed trying to put it together, and the file was
> >corrupted.
> >Luckily, I always save them separately as tifs, and stitched those
> >together. For ease of handling, I collapsed z and stitched maximum
> >intensity projections (and extended depth of field for DIC, using the BIG
> >Lausanne's plugin) together for the big picture, using 3D stitching for
> >smaller ROIs. MosaicJ works fine, as does Stephan Preibisch's.
> >StackReg (BIG Lausanne) often works ok (I only stick with Translation or
> >rigid body, never scaled or affine for obvious reasons). Especially useful
> >is a version using StackReg, called MultiStackReg or MultiStackRegFix
> >(Brad
> >Busse/Ping Fu & Jennifer Staab, resp.), allow saving the transformation
> >matrix for one channel and aligning the next using those parameters. I'd
> >like to do the same for the SIFT-based registration plugin (Stephan
> >Saalfeld), which mostly works really well (parameters sometimes need
> >adjusting) and often gets the job done where StackReg fails.
> >
> >Kind regards
> >
> >Philippe
> >
> >_____________________________________
> >Philippe Laissue, PhD, Bioimaging Manager
> >School of Biological Sciences, Room 4.17
> >University of Essex, Colchester CO4 3SQ, UK
> >(0044) 01206 872246 / (0044) 07842 676 456
> >
[hidden email]
> >
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZIGe> >V2W8npA&u=http%3a%2f%2fprivatewww%2eessex%2eac%2euk%2f%7eplaissue
> ><
>
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> >
> >
> >
> >
> >_____________________________________
> >Philippe Laissue, PhD, Bioimaging Manager
> >School of Biological Sciences, Room 4.17
> >University of Essex, Colchester CO4 3SQ, UK
> >(0044) 01206 872246 / (0044) 07842 676 456
> >
[hidden email]
> >
>
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> >
> >
> >On 3 April 2014 09:05, Straatman, Kees (Dr.) <
[hidden email]>
> wrote:
> >
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >>
> >>
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZID> >>LC32Z3pg&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalm
> >>icroscopy
> >> Post images on
> >>
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZIG> >>fDjWwj9g&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your
> >>posting.
> >> *****
> >>
> >> Dear Timothy,
> >>
> >> We recently had some problems with stitching using NIS-Elements which
> >>were
> >> resolved by calibrating the stage. The info I received from our Nikon
> >> product specialist was:
> >>
> >> "Go to the Calibration menu and objectives, there is an option on the
> >> right to recalibrate objective (ensure the correct objective is
> >>selected).
> >> In the wizard select the auto option, ensure you have a sample on the
> >>stage
> >> in focus with good detail. The software will run an autocalibrate and
> >> should then stitch correctly."
> >>
> >> This solved the problem for us. We also noticed that after the camera
> >>was
> >> slightly turned by accident the stitching did not work properly anymore
> >>and
> >> we needed to recalibrate.
> >>
> >> Best wishes
> >>
> >> Kees
> >>
> >>
> >> Dr Ir K.R. Straatman
> >> Senior Experimental Officer
> >> Centre for Core Biotechnology Services
> >> University of Leicester
> >>
> >>
> >>
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZID> >>aV3z8n9A&u=http%3a%2f%2fwww2%2ele%2eac%2euk%2fcolleges%2fmedbiopsych%2ffa
> >>cilities-and-services%2fcbs%2flite%2faif
> >>
> >>
> >>
> >>
> >> -----Original Message-----
> >> From: Confocal Microscopy List [mailto:
[hidden email]
> ]
> >> On Behalf Of Feinstein, Timothy
> >> Sent: 02 April 2014 19:11
> >> To:
[hidden email]
> >> Subject: Aligning large stacks
> >>
> >> *****
> >> To join, leave or search the confocal microscopy listserv, go to:
> >>
> >>
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZID> >>LC32Z3pg&u=http%3a%2f%2flists%2eumn%2eedu%2fcgi-bin%2fwa%3fA0%3dconfocalm
> >>icroscopy
> >> Post images on
> >>
>
http://scanmail.trustwave.com/?c=129&d=3eu904ma0h6a25H5kaVFITC-PSzasnHZIG> >>fDjWwj9g&u=http%3a%2f%2fwww%2eimgur%2ecom and include the link in your
> >>posting.
> >> *****
> >>
> >> Hello all,
> >>
> >> We have a number of folks who routinely test the limits of our A1-RS
> >> system by collecting for example large and high-resolution atlases of
> >> clarified brains (at least the 300 um -1 mm depth that we can reach
> >>with an
> >> inverted scope). Our coded stage and a software feature in Elements
> >>lets
> >> us create 3D stacks of very large images stitched together from 16 to
> >>100
> >> individual images per slice.
> >>
> >> We have found that the alignment can go slightly off from one slice to
> >>the
> >> next, screwing with our deconvolution and analysis results. This is
> >>not by
> >> itself shocking; these jobs are asking an awful lot of the system. We
> >>have
> >> the system pretty well isolated from vibration and air currents and
> >>nobody
> >> goes near it while collecting.
> >>
> >> Elements has an alignment feature built in but it does not produce great
> >> results from very large images (e.g. 4096 ^2 and up). I have tried the
> >> registration plugins menu in Fiji and my current favorite, StackReg, can
> >> produce solid results. Rigid body registration seems to do the job
> >>most of
> >> the time. On the other hand its progress bar is not very helpful and
> >>some
> >> alignments can take overnight to all weekend, if they work.
> >>
> >> So I thought it would help to throw this out to those of you who do this
> >> more often - do you have a favorite workflow for big-job registrations?
> >> Do
> >> you have a favorite freeware, Matlab plugin or paid option for these big
> >> jobs? Should I stop stitching the images and let the coded stage handle
> >> alignment on its own?
> >>
> >> We use a workstation with a decent graphics card and 36 GB of RAM. We
> >>can
> >> put in a lot more if that will help.
> >>
> >> Any advice on or off list would be appreciated.
> >>
> >> Thanks and all the best,
> >>
> >>
> >> TF
> >>
> >> Timothy Feinstein, Ph.D. | Confocal Manager
> >> 333 Bostwick Ave., N.E., Grand Rapids, Michigan 49503
> >> Phone: 616-234-5819 | Email:
[hidden email]<mailto:
> >>
[hidden email]>
> >>
>