converting Zeiss .lsm files to .czi

[Stephen Firth (Med)]

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Hi,
we are trying to convert 100+ large (35Gb), 5D files from .lsm to .czi, as
we cannot open these large files with Imaris (data points are scrambled
after ~ 90 timepoints).
This is possible with Zen and Zen lite but is time consuming at 20 min + to
open the file then again to save the file in the different format and there
seems to be no way to batch perform this task.
We've attempted written scripts for FIJI to allow export (i.e., batch
conversion) of these files as ome-tifs using Bio-Formats, but the
Bio-Formats exporter in FIJI doesn't currently support BigTiff, so the file
saving fails because the dataset is too large. We've also tried the
Bio-formats command-line converter, which does support BigTiff, but in it's
current incarnation it's very slow and inevitably crashes at some point
during the conversion of these large files.

Has anyone had this issue before?
Have you found a better way to do the conversion, or direct opening with
Imaris that does not scramble the file?
Cheers,
Stephen

--
Stephen Firth
Manager of Advanced Optical Microscopy
Monash Micro Imaging
Monash University

[Pascal Weber]

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I've had this kind of problem. The only way is to cut the file. But I have a full
version of ZEN for creating movies. My computer has 128 GB of ram 16 cores this
may explain it. But infact you export ZVI or LSM file with ZEN (i have the last
version) in any file format. Hope to see you again. Cheers. Pascal

[Christian Götze]

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COMMERCIAL POSTING!

Hi Stephen,

I don't know if you rely on Imaris completely. If you are free in your
tools, you could try our arivis Browser/arivis Vision 4D to handle your
data. Our software is intended to handle large data even on smaller PCs.
Arivis Vision 4D is the smaller version, just for visualization
purposes, the arivis Browser adds more advanced features as scripting,
extendibility and data analysis. Both can import LSM as well as CZI.

Arivis Vision 4D can be downloaded from our website as a fully
functional 14 days trial:
http://vision.arivis.com/en/arivis-Vision-4D

Best
Christian

--
Christian Götze
Unit Leader
Business Unit arivis Vision

Am 28.10.2013 09:14, schrieb Stephen Firth:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi,
> we are trying to convert 100+ large (35Gb), 5D files from .lsm to .czi, as
> we cannot open these large files with Imaris (data points are scrambled
> after ~ 90 timepoints).
> This is possible with Zen and Zen lite but is time consuming at 20 min +
> to
> open the file then again to save the file in the different format and
> there
> seems to be no way to batch perform this task.
> We've attempted written scripts for FIJI to allow export (i.e., batch
> conversion) of these files as ome-tifs using Bio-Formats, but the
> Bio-Formats exporter in FIJI doesn't currently support BigTiff, so the
> file
> saving fails because the dataset is too large. We've also tried the
> Bio-formats command-line converter, which does support BigTiff, but in
> it's
> current incarnation it's very slow and inevitably crashes at some point
> during the conversion of these large files.
>
> Has anyone had this issue before?
> Have you found a better way to do the conversion, or direct opening with
> Imaris that does not scramble the file?
> Cheers,
> Stephen
>

--
Christian Götze
Unit Leader
Business Unit arivis Vision

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