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

Posted by Christin Wittfoth on Nov 02, 2016; 8:43am
URL: http://imagej.273.s1.nabble.com/What-is-the-thing-with-Test-Block-matching-parameters-tp5017522.html

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]


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