Opening split microManager movies as one movie

bio-formats
storm
imagej
micro-manager

#1

Hello,

I do super resolution micrsocopy, which means lots of very long movies (several 10s of thousands of frames). When I acquire these movies, µManager will often split them into several individual movies once they get larger than 4 GB. They’re in the same folder, with the same name (except for the _1, _2 etc. that is added to the end of the new file) and the same metadata. Is there a better way to open these as a single movie than simply opening both and concatenating them? If so, how would one do this in a macro?

I thought there was an option to do this in bio-formats, but I haven’t found it yet.


#2

Hello, D_Virant

The file which from microManager is movie file?(not sequential image)
Converting a movie file to an image file, the converted data is very big .
I think many personal computers can not open 4GB movie files as image data.
How about saving captured image as sequential image in TIFF format?
And then, open the file of the range you are interested in.
*I do not know about microManager well, my answer may be misplaced.

hwada


#3

The movies are 4GB Tiff files. It’s several movies that belong together (same acquisition) and should be analyzed as one, but are split up by micromanager because they are too big.


#4

Hi @D_Virant,

the Bio-Formats Micro-Manager reader should have some support for acquired filesets distributed over multiple 4GB TIFF files. See for instance the sample fileset we are using in our non-regression testing.

A couple of immediate questions might help us identifying your issue:

  • is your fileset acquired with a companion metadata.txt file?
  • if so are you selecting the metadata file or one of the TIFF when opening the fileset?

See https://docs.openmicroscopy.org/bio-formats/5.9.0/users/micromanager/index.html for more information on how the Micro-Manager selects its reader depending on the fileset.

Best,
Sebastien