http://imagej.273.s1.nabble.com/What-is-the-thing-with-Test-Block-matching-parameters-tp5017522p5017534.html
for changing parameters: so thanks again. I will read it more carefully!
> 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.: +49 (0)3834 86- 4065
>> Fax: +49 (0)3834 86- 4067
>>
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlM.Sc. Christin Wittfoth