TrakEM2 - Import by text file

[Annette Web.de]

Dear colleagues,

 I'm trying to produce a mosaic out of 300 to 700 single images using TrakEM2. For the import I'm using a script (filename x y z). This actually worked pretty well some month ago.

But now I have problems by importing the images by text file.

Importing single tif files the images are shown like the originals (screen shot; image; top left) . using the script the images are absolutely dark (contrast, brightness?!) as shown in the screen shot.





I don't know what I'm doing wrong right now or what probably changed in the meantime.

Does anybody has an idea or has the same problems.

Thank a lot and best regards,

 

Annette

[Albert Cardona-2]

El 29 de febrer de 2012 16:28, Annette <[hidden email]> ha escrit:

> Dear colleagues,
>
>  I'm trying to produce a mosaic out of 300 to 700 single images using TrakEM2. For the import I'm using a script (filename x y z). This actually worked pretty well some month ago.
>
> But now I have problems by importing the images by text file.
>
> Importing single tif files the images are shown like the originals (screen shot; image; top left) . using the script the images are absolutely dark (contrast, brightness?!) as shown in the screen shot.
>
> I don't know what I'm doing wrong right now or what probably changed in the meantime.
>
> Does anybody has an idea or has the same problems.
>
> Thank a lot and best regards,

Dear Annette,

are the images 8-bit, 16-bit, 32-bit? How many channels? Do they have a LUT?

What changed in the interim is that the "Import from text file"
command doesn't load the while image files but only their file
headers. This approach saves lots of time, given that the whole image
file will be loaded shortly after to generate the mipmaps for
visualization.

What could have gone wrong: that for some reason, the new code doesn't
support your images well. Please answer the question above and I'll
get back to you.

Thanks for reporting on the issue.

Albert

--
http://albert.rierol.net
http://www.ini.uzh.ch/~acardona/