[OpenSPIM] Problems with Image Processing

[Johannes Schindelin]

Hi Dylan,

On 2015-06-09 14:45, Windell, Dylan wrote:

> I am very new to OpenSPIM and do not have previous experience with
> regards to coding or ImageJ so I do apologise for all the basic
> questions.
> 
> I have managed to take some practise stack image stacks at 6 angles
> (300 images - ~2-4GB) but they do not open normally in Image J and the
> program just says this:
> 
> Reading heading file header (Bio-Formats Import Options listing all
> series), Cancelling thumbnail generation, Import preparations complete
> - which is followed by nothing.
> 
> When I tried pre-processing the images using the macro I used the
> following adaptions to the code as I only have 1 time-point:
> 
> for ( t = 1; t <= 1; t++ ) {
>     for ( a = 0; a <= 5; a++ )
> 
> As I have Windows 7 64bit, I changed the directory to this:
> open("E:\\SPIM_Images\\<file:///\\E:\SPIM_Images\>....spim_TL"
> 
> I also attached an exception message I received when trying to process
> the files.

It appears as if the time lapse might have been interrupted (but this is 
just a wild guess).

You could try to open the files individually by using 
File>Import>Bio-Formats and then adjusting the setting so that it does 
*not* group the images.

Ciao,
Johannes