[OpenSPIM] Problems with Image Processing

[Windell, Dylan]

Hi Johannes,

Thank you for your email. I changed the settings to open the files without any prompts but it still seems to bring up all the different stacks every time I try to open a file or convert the file types. The files are actually converting now but they are taking >3 hours each and sometimes an error pops up telling me the file type incompatible and will not convert at all.

The macro only converts one at a time too, can it convert them all at once? Whenever I type in 'setBatchMode( true )' I get the attached error.

Furthermore, I also get this warning quite often: 'Could not get charToByteConverterClass!' Any idea what this is?

Thanks again,

Dylan

-----Original Message-----
From: Johannes Schindelin [mailto:johannes.schindelin at gmx.de]
Sent: 09 June 2015 14:02
To: Windell, Dylan
Cc: openspim at openspim.org
Subject: Re: [OpenSPIM] Problems with Image Processing

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
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