Thank you for your reply. I'm a very new user of TrakEM (and...not actually using it myself - just helping some other folk).
> On 12 Mar 2018, at 11:55 , Christian Goosmann <
[hidden email]> wrote:
>
> Hi Kenneth
>
> did you think of exporting your region of interest from trackEM. Draw a rectangle anywhere in the display, right click choosing 'export' and 'make flat image'. A dialog opens where you can specify which range of slices or "z-positions" you want. It either generates a stack as an open document or writes one to the disk, you choose.
>
> hth
>
> Christian
>
> ---
> Christian Goosmann
> Mikroskopie
> Max-Planck-Institut für Infektionsbiologie
> Campus Charité Mitte
> Charitéplatz 1
> 10117 Berlin
> Tel.: +49 30 28460 388
>
> On 10.03.2018 15:20, Kenneth Sloan wrote:
>> We are using TrakEM to look at a stack of EM images. It works great!
>>
>> But, we would like to generate orthogonal views of the stack of images.
>>
>> I am, alas, completely ignorant of how TrakEM manages the images (multiple tiles, multiple slices).
>>
>> It seems clear that the image displayed by ImageJ is not a "stack" as far as ImageJ is concerned.
>> Any attempt to select that window and apply any Stack command fails miserably ("must be a stack").
>> I didn't really think that would work, but I tried it.
>>
>> So...is there a way to produce a (perhaps low resolution, perhaps a limited "brick") stack that can be treated as a normal ImageJ stack of images, so that we could use (for example) "Orthogonal Views").
>>
>> I expect this will be expensive. The data set is 10-20TB. So, the key is probably "lower resolution or restricted region in x,y,z"
>>
>> --
>> Kenneth Sloan
>>
[hidden email]
>> Vision is the art of seeing what is invisible to others.
>>
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http://imagej.nih.gov/ij/list.html>
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