Batch convert Micro-manager files to TIFF stacks?

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Batch convert Micro-manager files to TIFF stacks?

Stanislav Vitha
I have dozens of MicroManager z-stacks that I would like to convert
to the regular multi-tiff stacks of ImageJ for further batch
processing and analysis (by a commercial software). Is there a way to
do the conversion in a batch mode? I tried to modify an existing
batch process macro to use the "Open Micro-manager File" plugin, but
there does not seem to be a way to pass the file (or actually a
folder) name to be opened to this plugin, so it always brings up the
"Open" dialogue.

I also tried the "Open Micro-manager File" plugin in the batch mode
of ImageJ (Process-Batch-Macro) pasting  run(" Open Micro-Manager
File") in the macro field, but that does not do anything.

Thanks a lot!

Stan Vitha

Microscopy and Imaging Center
Texas A&M University
BSBW 119
College Station, TX 77843-2257

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