Re: What is the thing with "Test Block matching parameters"?

Posted by Saalfeld, Stephan on Nov 03, 2016; 6:20pm
URL: http://imagej.273.s1.nabble.com/What-is-the-thing-with-Test-Block-matching-parameters-tp5017522p5017533.html

Hi Christin,

blind shot.  Try this:

To perform a pre-alignment we used as parameters:

steps per scale octave: 3
minimum image size: 256
maximum image size: 1024
feature extraction threads: 3
maximal alignment error: 50
minimal inlier ratio: 0
minimal numbers of inliers: 5
expected transformation: Rigid
test multiple hypotheses: yes
test max. 3 layers, give up after 3 failures
desired transformation: Affine
regularize: yes -> Rigid, lambda 0.1
maximal iterations: 1000
plateauwidth: 200

Why?  Section 3 appears to be unaligned to the rest of the stack.  If
that could be fixed, search for elastic distortion becomes a lot
simpler and faster.  Then:

Test Blockmatching:

layer scale: 0.25
search radius: 50
block radius: 75
resolution: 30
smoothness filter (yes)
approximate local transformation: Rigid
local region sigma: 150
maximal local displacement - absolute: 20
- relative: 3

yet, this may be wrong, depending on what happened before.  Did you
read

http://imagej.net/Test_Block_Matching_Parameters

?  That Wiki-page explains what the colors and blackness mean.

Best,
Stephan





On Wed, 2016-11-02 at 09:43 +0100, Christin Wittfoth wrote:

> Hi everyone,
>
> we try to find out how to do an elastic alignment but we despair of 
> testing block matching parameters in TrakEM2. We are not sure how to 
> interpret the results and to decide if we have found the right 
> parameters. We attached one snapshot as example:
> - Is the size of the black area important? (smaller <-> bigger)
> - What do the colours mean?
> - How important is the blackness of the colours? (Compare the middle
> row 
> and column which show bright colours but in complementary ones of
> the 
> colour range)
> - We have read the parameters which are defined in pixels depend on
> the 
> image size. But in which range can we test the parameters to get a 
> successful alignment?
> - What does the layer scale mean and is depending on?
> - Can we use information out of the log? (We noticed the log name a 
> "maximum local displacement", for example.)
>
> The size of the images was 3000 x 2250 px.
>
> To perform a pre-alignment we used as parameters:
>
> steps per scale octave: 3
> minimum image size: 256
> maximum image size: 1024
> feature extraction threads: 3
> maximal alignment error: 225
> minimal inlier ratio: 0.05
> minimal numbers of inliers: 15
> expected transformation: Affine
> test multiple hypotheses (max. 3 layers, give up after 3 failures)
> desired transformation: Rigid
> maximal iterations: 1000
> plateauwidth: 200
>
> We exported the flat images by using a scale of 50 % and tested the 
> block matching parameters:
>
> layer scale: 0.33
> search radius: 115
> block radius: 145
> resolution: 30
> approximate local transformation: Rigid
> local region sigma: 65
> maximal local displacement - absolute: 135
> - relative: 35
>
>
> We are grateful for every help!
>
> Greetings,
> Christin & Tina
>
> ------------------------------------------------------------
>
> M.Sc. Christin Wittfoth
>
> Cytologie und Evolutionsbiologie
> Universität Greifswald
> Zoologisches Institut und Museum
> Soldmannstrasse 23
> Haus 6.1
> D - 17487 Greifswald
> Tel.: [phone]
> Fax: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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