Leica LAS-AF tif export

[Gordon Smith]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

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

[Gabriel Krens]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

I think the most simple manner to convert LAS files is to use FIJI bio-formats
importer and save them in the desired format from FIJI/Image-J

[Smith, Benjamin E.]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

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
________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Gordon Smith [[hidden email]]
Sent: Wednesday, August 19, 2015 5:33 AM
To: [hidden email]
Subject: Leica LAS-AF tif export

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

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

[Rubin]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
Post images on http://www.imgur.com and include the link in your posting.
*****

Hi Gordon,

We have the same problem as you. The LAS-AF doesn't support saving files
while imaging, so we have to spend some time in saving files after imaging.
We found one way to make this process faster is to save Lif file to a big
SSD (800GB). Once it is saved, we can start imaging again. Then we transfer
the Lif file to another computer with LAS-AF lite installed to export to
TIFs. It does take hours to finish if you have a file larger than 100GB.


Guobin Sun


On Wed, Aug 19, 2015 at 5:57 AM, Smith, Benjamin E. <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> 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
> ________________________________________
> From: Confocal Microscopy List [[hidden email]] on
> behalf of Gordon Smith [[hidden email]]
> Sent: Wednesday, August 19, 2015 5:33 AM
> To: [hidden email]
> Subject: Leica LAS-AF tif export
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> 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
>