MBF ImageJ importing movies and creating a stack

[Cheuk Tam]

Dear ImageJ Community,

I recently tried to use MBF ImageJ to import a sequence of images and
ultimately use an existing stack (an AVI file) or creat one using the
Image>Stacks>Images to Stack function.  I've had trouble with both.  On my
work Mac, the memory limit only allows 18 frames to open.  When I try to
change the memory limit, the program does not allow me to.  When I try to
open all the 300 images I want to make into a stack, the Bio-Formats Import
Options pop-up menu shows up after each image opens and will not proceed
unless I manually click OK each time.  This didn't happen when I used the
MBF ImageJ about 8 months ago.  Has there been a change in the ImageJ core
or the MBF version?  Thank you for your help.

Best,
Cheuk

[Melissa Linkert-2]

Hi Cheuk,

> I recently tried to use MBF ImageJ to import a sequence of images and
> ultimately use an existing stack (an AVI file) or creat one using the
> Image>Stacks>Images to Stack function.  I've had trouble with both.  On my
> work Mac, the memory limit only allows 18 frames to open.

Have you tried opening the files as a virtual stack?  The Bio-Formats
importer has a "Use virtual stack" option, as does ImageJ's
"File > Import > AVI" command.

> When I try to
> change the memory limit, the program does not allow me to.

If you haven't already, you might have a look at the instructions for
increasing the memory limit in ImageJ here:

http://imagejdocu.tudor.lu/doku.php?id=faq:technical:how_do_i_increase_the_memory_in_imagej

If those instructions don't help, then it would be a good idea to mention which
operating system you are using, how you tried to increase the memory, and any
error messages that you see.

> When I try to
> open all the 300 images I want to make into a stack, the Bio-Formats Import
> Options pop-up menu shows up after each image opens and will not proceed
> unless I manually click OK each time.

If the files are named numerically (e.g. image001, image002, image003, ...),
then you should be able to open any one of the files and check the
"Group files with similar names" option in the "Bio-Formats Import
Options" window.  This will group together any similarly-named files
into a single dataset - with any luck, all 300 images will automatically
appear in a single stack.

> This didn't happen when I used the
> MBF ImageJ about 8 months ago.  Has there been a change in the ImageJ core
> or the MBF version?

It may be that you previously had Bio-Formats configured to use the
"windowless import" option, which bypasses the options window whenever
Bio-Formats is used.

To use this option just once, select
"Plugins > LOCI > Bio-Formats Windowless Importer".  To use this option
by default for files of a particular format, select "Plugins > LOCI >
LOCI Plugins Configuration", then select the format of the files that
are working with from the list on the left, and then check the
"Windowless" box.

Regards,
-Melissa

On Thu, Jul 28, 2011 at 03:09:05PM -0700, Cheuk Tam wrote:

> Dear ImageJ Community,
>
> I recently tried to use MBF ImageJ to import a sequence of images and
> ultimately use an existing stack (an AVI file) or creat one using the
> Image>Stacks>Images to Stack function.  I've had trouble with both.  On my
> work Mac, the memory limit only allows 18 frames to open.  When I try to
> change the memory limit, the program does not allow me to.  When I try to
> open all the 300 images I want to make into a stack, the Bio-Formats Import
> Options pop-up menu shows up after each image opens and will not proceed
> unless I manually click OK each time.  This didn't happen when I used the
> MBF ImageJ about 8 months ago.  Has there been a change in the ImageJ core
> or the MBF version?  Thank you for your help.
>
> Best,
> Cheuk