Micromanager 2.0 gamma Image Stack won't exceed 4 GB

Hi, I’m running multi-D acquisition on micro-manager-2.0gamma to get 10,000 frames of tiff file on a single stack. In doing this, I realized that micromanager saves piles of tiff files having 4 GB size of each pile, containing about 427 frames, instead of a single large tiff file that contains all 10000 frames.
Is there any way to save all acquired tiff files on a single stack?
Thanks in advance.

Unfortunately, the Tiff format has a maximum size of 4 GB (since the internal pointers are 32-bit). There is another format, BigTiff, which gets around this, but micro-manager does not support it

Is there a reason you want them in one large stack? Micro-Manager will automatically open them as one stack, and BioFormats in Fiji also will combine them.

When I want to image a cell for some period of time at a fixed z-height, or take image at different z-position continuously, the frame numbers becomes large and file size exceeds 4 GB. It would be easy to see all of those large frames as a single movie. Even for the camera categorization, we need to take a long series of files in one stack, right?
Do you mean the separate stacks of tiff files could be open as single stack from Micro-Manager or BioFormats in Fiji could do that?

Yeah, of course I understand why you want to record long movies. :slight_smile: I’m asking why you want them to be saved as one file.

Try opening one of the files in Micro-Manager. It should open the entire experiment, not just one 4-GB file. BioFormats should, too, but you may need to check the “concatenate series when compatible” and “open all series” options (and maybe “group files by similar filename”—sorry, I forget the details at the moment). Test these out and see if they have the right number of frames and channels and positions after you open.



Thank you very much Sam. I think your reply triggered me to figure out a way.

I was wondering how could I open all the image sequence in a single windows when they are saved in a different piles.
When I open these individual files in Micro-Manager as “File”>“Open”>“File name”, they would open only a single 4 GB file of 427 frames. However, I now realized that, if I open files as “File”>“Import”>“Image Sequence”> “File name”, then it promotes to a window with option to choose how many pictures to load and which picture to start from. This way opened entire image files in a single window.

Is this the way you are mentioning above? Or, am I doing anything mix-up here?

Usually, the whole dataset opens in Micro-Manager. If it doesn’t, something is wrong. You may need to open it using File > Open Virtual if you do not have enough RAM. Make sure that you use the File > Open from the Micro-Manager menu, not the one from the ImageJ menu.

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Yes, it worked. Thanks.