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

[Christin Wittfoth]

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

--
------------------------------------------------------------

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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Christin Wittfoth]

Sorry, I forgot the snapshot...


Am 19.10.2016 um 16:33 schrieb Christin Wittfoth:

> 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
>

--
------------------------------------------------------------

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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Saalfeld, Stephan]

Hi Christin,

can you also share the parameters used, the size of the images, the
scale of the export, and the parameters used for rigid or affine
alignment?

Best,
Stephan

On Wed, 2016-10-19 at 16:35 +0200, Christin Wittfoth wrote:

> Sorry, I forgot the snapshot...
>
>
> Am 19.10.2016 um 16:33 schrieb Christin Wittfoth:
> >
> > 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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