Import image sequence of unequal size in TrackEM

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Import image sequence of unequal size in TrackEM

Jeremias Brand
Dear ImageJ List users,

I have a stack of .dm3 images from serial block face SEM imaging. Since
aquisition time is limited by image size I start aquisition with small
image size (4500px x 4500px) and once my object becomes bigger I adjust
to larger images (up to 8000px x 8000px).
I now want to import these images as a sequence with one image per z
layer. To do this I followed the trackEM tutorial and tried:

Import -> Import Sequences as grid...; then I set number of rows: 1,
number of columns: 1, number of slices: <number of images I am importing>.

TrackEm then starts importing but as soon as the image dimensions change
I get this error:

Size mismatch! (see attached image)

Selecting either 'ignore all' or 'fix all' both do not resolve the
issue, because the error apears for every slice that does not match the
original image, which are too many to click the message individually
(about 800 images).

Is there any other way of importing a sequence of images of unequal size
into TrackEM?

Thank you for your help,

Jeremias Brand

PhD Student
Evolutionary Biology
Department of Environmental Sciences
University of Basel






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Re: Import image sequence of unequal size in TrackEM

Saalfeld, Stephan
Hi Jeremias,

please make a text file like this

filename1 0 0 0
filename2 0 0 1
filename3 0 0 3

...


and "import from text file".

Excel can generate such text files (save as CSV) or you script it.

This question has been answered mmany times in this forum and elsewhere
but web-search is stil hampered by lack of AI.  Use "import from text
file trakem2" in Google and try to get the spelling right ;).

Cheers,
Stephan


On Thu, 2017-06-01 at 23:22 +0200, Jeremias Brand wrote:

> Dear ImageJ List users,
>
> I have a stack of .dm3 images from serial block face SEM imaging.
> Since 
> aquisition time is limited by image size I start aquisition with
> small 
> image size (4500px x 4500px) and once my object becomes bigger I
> adjust 
> to larger images (up to 8000px x 8000px).
> I now want to import these images as a sequence with one image per z 
> layer. To do this I followed the trackEM tutorial and tried:
>
> Import -> Import Sequences as grid...; then I set number of rows: 1, 
> number of columns: 1, number of slices: <number of images I am
> importing>.
>
> TrackEm then starts importing but as soon as the image dimensions
> change 
> I get this error:
>
> Size mismatch! (see attached image)
>
> Selecting either 'ignore all' or 'fix all' both do not resolve the 
> issue, because the error apears for every slice that does not match
> the 
> original image, which are too many to click the message individually 
> (about 800 images).
>
> Is there any other way of importing a sequence of images of unequal
> size 
> into TrackEM?
>
> Thank you for your help,
>
> Jeremias Brand
>
> PhD Student
> Evolutionary Biology
> Department of Environmental Sciences
> University of Basel
>
>
>
>
>
>
> ---
> Diese E-Mail wurde von Avast Antivirus-Software auf Viren geprüft.
> https://www.avast.com/antivirus
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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