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

Posted by Christin Wittfoth on Oct 19, 2016; 2:33pm
URL: http://imagej.273.s1.nabble.com/What-is-the-thing-with-Test-Block-matching-parameters-tp5017422.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.)

We are grateful for every help!

Greetings,
Christin & Tina

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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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