http://imagej.273.s1.nabble.com/Multiview-Reconstruction-Plugin-Help-tp5016784p5016793.html
>Hi Neil,
>
>I gave a short tutorial at Janelia this week which was recorded and I
>will try to make it accessible as soon as possible. In the meantime, I am
>trying to answer some of your questions.
>
>How do you import the data into the Multiview Reconstruction? If it is
>via loading the CZI dataset, then, yes, it should apply the approximate
>rotation already. It does not really matter around which point it rotates
>as the matching is done translation-invariant. However, for other
>datasets (e.g. TIFFs) one needs to figure out the right rotation (x-axis
>or y-axis, e.g. +90 or -90 degrees), which depends on the microscope
>itself. I recently added a simple center of mass alignment which might
>help as after applying a transformation it can more or less overlap the
>views. I realise that there should maybe be a tool that helps figuring
>this out using Max-Intensity projections in all potentially correct
>orientations. It is on the to-do list now.
>
>The following parameters mostly are a tradeoff between the likelihood of
>the transformation identified being correct and identifying a
>transformation at all:
>
>Fix Tiles Š Usually one tile/view/stack is not modified during global
>optimization. My suggestions is to not change this if you do not
>understand the details of the global optimization procedure.
>Map Back Š Only matters if no tile/view/stack is fixed
>
>Transformation Model - Affine/Rigid/Translation Š well, that depends on
>the task. Usually Affine, regularised with Rigid makes most sense
>Number of Neighbours Š More neighbours gives more reliable, but less
>matching descriptors (check out the video of my presentation on the
>principle:
>
https://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fwww.youtu>be.com%2fwatch%3fv%3dIupXS_On2rg&data=01%7c01%7ctnf8%40pitt.edu%7c4ee6e23f
>893a4cbe6b4808d3a1b861a1%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=WB5m
>Ta3CVM%2fz7MvJHzxGY5bwBgAJumx4tbZaikdFTT8%3d)
>Redundancy Š Tolerante potential misdetected blobs - more redundancy will
>find more potential matches, but is slower and might find more that are
>not correct
>Significance (N-times) Š For each descriptor we find the best matching
>and second best matching one in the other view. We consider it a
>potential match if the best one is N-times better than the second best
>one. So a higher number results in more reliable matches, a lower number
>in more matches - play with this one first if you identify no
>transformation model
>Allowed RANSAC error Š All potentially corresponding descriptors of two
>views are subject to a (transformation in this case) model-based outlier
>removal, where this is the maximally allowed error so it still is
>considered as ³agreeing² on the same model. Keep in mind that sometimes
>the z-resolution is way worse than xy - this pixel error is isotropic
>coordinates, so usually in xy pixel units.
>
>Cheers,
>Stephan
>
>---
>
>Dr. Stephan Preibisch
>Group Leader
>
>Berlin Institute of Medical Systems Biology of the MDC
>Building 89, 1.08b
>
>email:
>
[hidden email]<mailto:
[hidden email]>
>web:
>
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>
>On 30 Jun 2016, at 20:11, Anthony, Neil
><
[hidden email]<mailto:
[hidden email]>> wrote:
>
>Hi guys, I hope the data treats you well.
>
>I've been playing around with some SPIM data and the multiview
>reconstruction plugin. I've been having trouble registering some data
>sets from some cleared tissue data sets that fill the field of view, and
>hence I have no registration beads to work with.
>
>I've been trying to use the redundant geometric local descriptor matching
>option for the type of registration in the basic registration options,
>which I assume is the correct option (I recall hearing Stephan mention it
>in his tutorial presentation). On the
>ImageJ.net<<a href="https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2">https://na01.safelinks.protection.outlook.com/?url=http%3a%2f%2
>fimagej.net&data=01%7c01%7ctnf8%40pitt.edu%7c4ee6e23f893a4cbe6b4808d3a1b86
>1a1%7c9ef9f489e0a04eeb87cc3a526112fd0d%7c1&sdata=3xjyu%2b1DYZu9fgXM8WHQAsx
>b8RQrl%2bGm%2b3ZLkncueXU%3d> help page I see that it requires the info on
>the rotations. It knows the angles, and so I'm not sure if it already
>applies the rotations for me...? On using the apply transformations tool
>to rotation each data set the required amount around the x-axis I see in
>the BigDataViewer that it rotates on the corner of the volume. Does the
>translation-invariance mean that the volumes can be translated but not
>rotated? I also tried around the y-axis in case I had them mixed up but
>I saw something equally 'star shaped' in the BigDataViewer. Any tips on
>the manual transformation controls would be very helpful.
>
>In the following windows there are many options which I am equally unsure
>about. Any info on the nitty gritty of all the options and parameters
>would be much appreciated (Fix Tiles, Map back, Transform model,
>Regularization model and settings, and then the regularization settings
>too). Alternatively, if it's an option, if anybody has any documents
>and/or presentations on the related topics to help bring me up to speed
>that would be great. I've started to read some
>
>
>Thanks in advance for your time.
>
>Neil
>
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