Leica LIF batch processing help

[AdamC]

I'm trying to find a way to batch convert Leica LIF files.
At the moment I'm using the Live Data Mode on the Leica software to  
generate multi-position 4D stacks. The software, for some reason  
currently gives you 1 LIF file for this (in our case 2-3Gb) within  
which are the data is split into multiple experiments for each  
position (one per time point). So for 3 positions the LIF file looks  
like:

Stack for Position 1, Time point 1
Stack for Position 2, Time point 1
Stack for Position 3, Time point 1
Stack for Position 1, Time point 2  etc...

So for 3 positions with 100 time points each you would get 300  
separate experiments in the LIF file.

I can get the LOCI Bio-formats plugin to open each experiment  
individually, but I haven't found a way of getting it to either  
concatenate all of the time points for each position (so giving 1  
file per position) or to batch convert each position to into a TIF  
series (which would be easier to manipulate). At the moment we're  
using lots of microscope time exporting the entire LIF stack to TIFFs  
(loosing the metadata in the process, and especially loosing the  
record of the time interval)

Has anyone had any experience with this, or does anyone have any good  
suggestions.

Thanks

Adam


Dr Adam Cliffe
Research Fellow
Rørth Lab
Cell Migration Group
Temasek Lifescience Laboratory
1 Research Link
National University of Singapore
Singapore 117604

tel: [phone]
fax: [phone]

[lechristophe]

Dear Adam,

You can download a macro I wrote to extract images from .lif and .lei
files directly to .tif stacks, one stack for each channel. The macro
is made for simple xyz stacks, not multi-position or time-lapse stacks
but fiddling with the BioFormats macro extensions (a bunch of macro
commands that manipulate the data) will hopefully help you to do so by
modifying this macro. The macro batch processes all .lei and .lif
files found in one folder. Several options are available : background
substraction, filtering (mean,median, gaussian, sigma). One can choose
between several options for saving and displaying the result images.
Of course you need the BioFormats plugin installed.

Get it here :

https://www.bio.espci.fr/upload/files/LZS_Extractor_1.1.txt

If someone is interesed, I also have a version that can batch project
the stacks after processing.

Christophe

On Wed, May 14, 2008 at 8:06 AM, Adam Cliffe <[hidden email]> wrote:

> I'm trying to find a way to batch convert Leica LIF files.
>  At the moment I'm using the Live Data Mode on the Leica software to
> generate multi-position 4D stacks. The software, for some reason currently
> gives you 1 LIF file for this (in our case 2-3Gb) within which are the data
> is split into multiple experiments for each position (one per time point).
> So for 3 positions the LIF file looks like:
>
>  Stack for Position 1, Time point 1
>  Stack for Position 2, Time point 1
>  Stack for Position 3, Time point 1
>  Stack for Position 1, Time point 2  etc...
>
>  So for 3 positions with 100 time points each you would get 300 separate
> experiments in the LIF file.
>
>  I can get the LOCI Bio-formats plugin to open each experiment individually,
> but I haven't found a way of getting it to either concatenate all of the
> time points for each position (so giving 1 file per position) or to batch
> convert each position to into a TIF series (which would be easier to
> manipulate). At the moment we're using lots of microscope time exporting the
> entire LIF stack to TIFFs (loosing the metadata in the process, and
> especially loosing the record of the time interval)
>
>  Has anyone had any experience with this, or does anyone have any good
> suggestions.
>
>  Thanks
>
>  Adam
>
>
>  Dr Adam Cliffe
>  Research Fellow
>  Rørth Lab
>  Cell Migration Group
>  Temasek Lifescience Laboratory
>  1 Research Link
>  National University of Singapore
>  Singapore 117604
>
>  tel: [phone]
>  fax: [phone]
>

[aparna sadananda]

hi,
I have a question concerning a problem similar to the one described by
Dr.Adam. I have a z-stack of fruit fly embryo imaged  at different time
points and saved as an .oib fileby Olympus Fluoview. When I export these
files in TIFF format, I get a series of 100 or more images which then have
to be sorted. Is there a way to sort these files faster?
thanks in advance,
Aparna.
On Wed, May 14, 2008 at 1:13 PM, Christophe Leterrier <
[hidden email]> wrote:

> Dear Adam,
>
> You can download a macro I wrote to extract images from .lif and .lei
> files directly to .tif stacks, one stack for each channel. The macro
> is made for simple xyz stacks, not multi-position or time-lapse stacks
> but fiddling with the BioFormats macro extensions (a bunch of macro
> commands that manipulate the data) will hopefully help you to do so by
> modifying this macro. The macro batch processes all .lei and .lif
> files found in one folder. Several options are available : background
> substraction, filtering (mean,median, gaussian, sigma). One can choose
> between several options for saving and displaying the result images.
> Of course you need the BioFormats plugin installed.
>
> Get it here :
>
> https://www.bio.espci.fr/upload/files/LZS_Extractor_1.1.txt
>
> If someone is interesed, I also have a version that can batch project
> the stacks after processing.
>
> Christophe
>
> On Wed, May 14, 2008 at 8:06 AM, Adam Cliffe <[hidden email]> wrote:
> > I'm trying to find a way to batch convert Leica LIF files.
> >  At the moment I'm using the Live Data Mode on the Leica software to
> > generate multi-position 4D stacks. The software, for some reason
> currently
> > gives you 1 LIF file for this (in our case 2-3Gb) within which are the
> data
> > is split into multiple experiments for each position (one per time
> point).
> > So for 3 positions the LIF file looks like:
> >
> >  Stack for Position 1, Time point 1
> >  Stack for Position 2, Time point 1
> >  Stack for Position 3, Time point 1
> >  Stack for Position 1, Time point 2  etc...
> >
> >  So for 3 positions with 100 time points each you would get 300 separate
> > experiments in the LIF file.
> >
> >  I can get the LOCI Bio-formats plugin to open each experiment
> individually,
> > but I haven't found a way of getting it to either concatenate all of the
> > time points for each position (so giving 1 file per position) or to
> batch
> > convert each position to into a TIF series (which would be easier to
> > manipulate). At the moment we're using lots of microscope time exporting
> the
> > entire LIF stack to TIFFs (loosing the metadata in the process, and
> > especially loosing the record of the time interval)
> >
> >  Has anyone had any experience with this, or does anyone have any good
> > suggestions.
> >
> >  Thanks
> >
> >  Adam
> >
> >
> >  Dr Adam Cliffe
> >  Research Fellow
> >  Rørth Lab
> >  Cell Migration Group
> >  Temasek Lifescience Laboratory
> >  1 Research Link
> >  National University of Singapore
> >  Singapore 117604
> >
> >  tel: [phone]
> >  fax: [phone]
> >
>

[ctrueden]

Hi Adam & Aparna,

As Christophe said, you can use an ImageJ macro together with the
Bio-Formats plugins to batch convert LIF and OIB files to TIFF, as well as
perform various operations while doing so. By tweaking the macro, you have
flexible control over what happens to the data as part of the conversion.

If all you want to do is batch convert LIF or OIB to a more open format,
another option is the Bio-Formats "bfconvert" command line tool. By
specifying ".ome.tif" as the output file extension, you can convert your
data to OME-TIFF which includes preservation of multiple image series within
each file. It is as simple as:

bfconvert my-input-data.lif my-output-data.ome.tif

And you can use a Unix shell script or Windows batch file to automatically
process many files.

There are other approaches as well; if these solutions do not meet your
needs, let us know and we can offer additional suggestions.

-Curtis

On Wed, May 14, 2008 at 6:39 AM, aparna sadananda <[hidden email]>
wrote:

> hi,
> I have a question concerning a problem similar to the one described by
> Dr.Adam. I have a z-stack of fruit fly embryo imaged  at different time
> points and saved as an .oib fileby Olympus Fluoview. When I export these
> files in TIFF format, I get a series of 100 or more images which then have
> to be sorted. Is there a way to sort these files faster?
> thanks in advance,
> Aparna.
> On Wed, May 14, 2008 at 1:13 PM, Christophe Leterrier <
> [hidden email]> wrote:
>
> > Dear Adam,
> >
> > You can download a macro I wrote to extract images from .lif and .lei
> > files directly to .tif stacks, one stack for each channel. The macro
> > is made for simple xyz stacks, not multi-position or time-lapse stacks
> > but fiddling with the BioFormats macro extensions (a bunch of macro
> > commands that manipulate the data) will hopefully help you to do so by
> > modifying this macro. The macro batch processes all .lei and .lif
> > files found in one folder. Several options are available : background
> > substraction, filtering (mean,median, gaussian, sigma). One can choose
> > between several options for saving and displaying the result images.
> > Of course you need the BioFormats plugin installed.
> >
> > Get it here :
> >
> > https://www.bio.espci.fr/upload/files/LZS_Extractor_1.1.txt
> >
> > If someone is interesed, I also have a version that can batch project
> > the stacks after processing.
> >
> > Christophe
> >
> > On Wed, May 14, 2008 at 8:06 AM, Adam Cliffe <[hidden email]> wrote:
> > > I'm trying to find a way to batch convert Leica LIF files.
> > >  At the moment I'm using the Live Data Mode on the Leica software to
> > > generate multi-position 4D stacks. The software, for some reason
> > currently
> > > gives you 1 LIF file for this (in our case 2-3Gb) within which are the
> > data
> > > is split into multiple experiments for each position (one per time
> > point).
> > > So for 3 positions the LIF file looks like:
> > >
> > >  Stack for Position 1, Time point 1
> > >  Stack for Position 2, Time point 1
> > >  Stack for Position 3, Time point 1
> > >  Stack for Position 1, Time point 2  etc...
> > >
> > >  So for 3 positions with 100 time points each you would get 300
> separate
> > > experiments in the LIF file.
> > >
> > >  I can get the LOCI Bio-formats plugin to open each experiment
> > individually,
> > > but I haven't found a way of getting it to either concatenate all of
> the
> > > time points for each position (so giving 1 file per position) or to
> > batch
> > > convert each position to into a TIF series (which would be easier to
> > > manipulate). At the moment we're using lots of microscope time
> exporting
> > the
> > > entire LIF stack to TIFFs (loosing the metadata in the process, and
> > > especially loosing the record of the time interval)
> > >
> > >  Has anyone had any experience with this, or does anyone have any good
> > > suggestions.
> > >
> > >  Thanks
> > >
> > >  Adam
> > >
> > >
> > >  Dr Adam Cliffe
> > >  Research Fellow
> > >  Rørth Lab
> > >  Cell Migration Group
> > >  Temasek Lifescience Laboratory
> > >  1 Research Link
> > >  National University of Singapore
> > >  Singapore 117604
> > >
> > >  tel: [phone]
> > >  fax: [phone]
> > >
> >
>

[StellaIJ]

Dear Christoph,

I would need exactly the plugin you described, but I cannot access it.
Could you make it accessable to the public or post it here?

Thanks,

Stella