Posted by
Smith, Benjamin E. on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Leica-LAS-AF-tif-export-tp7584128p7584129.html
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Is it possible to save the data across several individual lif files? This spring we did 48 hours of 3D live imaging for 12+ pupae in a single run. To both protect the data, and keep the saves manageable, the data was saved at 5 points during the imaging. I then wrote a quick ImageJ macro that would read the lifs, process the stacks, down sample the data and stitch the files back together, so that the data was much more manageable out the other end.
-Ben Smith
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Sent: Wednesday, August 19, 2015 5:33 AM
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Subject: Leica LAS-AF tif export
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Hi everyone,
We're running large tile scans on a Leica, using LAS-AF software, and are having trouble
efficiently exporting the individual images as tifs. The total image set tends to be around 100
GB, and the manual export time tends to be several hours, during which the software is not
responsive and the scope is non-operational. Saving to a .lif file for later offline export to
individual tifs isn't any faster, and the AutoExporter module appears to act in the same
manner (although I haven't actually been able to AutoExport scans this large - maybe I didn't
wait long enough).
Does anyone have any advice to speed this up or get the saving / exporting to happen offline
so we can spend more time imaging and less time waiting for the software?
One option I've considered is trying to work with the .tmp file LAS-AF creates during the scan,
in which the actual incoming data is stored. Since this file is already on the disk when the scan
ends, presumably it could be a means to move the export process offline. Has anyone had any
experience working with, or re-opening the .tmp files created by LAS-AF?
Thanks,
Gordon Smith