Mosaic with optical sectoning

[Rachael Lim]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi! We are trying to run an experiment that requires image acquisition of a
very large area (a slice of rat brain; we use mosaic for this purpose),
along with optical sectioning.

However, the software that we are currently using does not allow us to
acquire both mosaic and optical sectioning simultaneously due to the
extremely large file size produced (about 2GB), which cannot be processed by
the software (software limitation of file size is 200MB).

I am wondering if it is possible for us to acquire the mosaic and optical
sectioning separately (i.e. mosaic for every plane of interest), export out
and compile them with another software. Does any of you have any suggestion
of possible software that has the capability of compiling individual planes
into a stack?

Please advise. Thank you!

Cheers,
Rachael Lim

[Rietdorf, Jens]

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http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Dear Rachael Lim,

Imaris (bitplane AG) has recently implemented functionality to handle huge image files (no commercial interest from my side). If you want to just merge the mosaics into a projection image, this could already be achieved with -for example- ImageJ. Aaron Ponti from our group has recently developed (MatLab based) software for a 3d alignment and shading correction of stacks from mosaics.

Dont hesitate to contact me for further detail.

Cheers, jens

Dr. Jens Rietdorf
head of microscopy unit
Friedrich-Miescher-Institute, wro-1066.2.32
Maulbeerstr.66, CH-4058 Basel, Switzerland
http://www.fmi.ch/  Phone [phone]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]On
Behalf Of Rachael Lim
Sent: Wednesday, October 17, 2007 9:57 AM
To: [hidden email]
Subject: Mosaic with optical sectoning


Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi! We are trying to run an experiment that requires image acquisition of a
very large area (a slice of rat brain; we use mosaic for this purpose),
along with optical sectioning.

However, the software that we are currently using does not allow us to
acquire both mosaic and optical sectioning simultaneously due to the
extremely large file size produced (about 2GB), which cannot be processed by
the software (software limitation of file size is 200MB).

I am wondering if it is possible for us to acquire the mosaic and optical
sectioning separately (i.e. mosaic for every plane of interest), export out
and compile them with another software. Does any of you have any suggestion
of possible software that has the capability of compiling individual planes
into a stack?

Please advise. Thank you!

Cheers,
Rachael Lim

[mmodel]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hello Rachael,

With ImageJ you can form a stack from individual images and then display
them as a mosaic.

Mike Model

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Rachael Lim
Sent: Wednesday, October 17, 2007 3:57 AM
To: [hidden email]
Subject: Mosaic with optical sectoning

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi! We are trying to run an experiment that requires image acquisition
of a
very large area (a slice of rat brain; we use mosaic for this purpose),
along with optical sectioning.

However, the software that we are currently using does not allow us to
acquire both mosaic and optical sectioning simultaneously due to the
extremely large file size produced (about 2GB), which cannot be
processed by
the software (software limitation of file size is 200MB).

I am wondering if it is possible for us to acquire the mosaic and
optical
sectioning separately (i.e. mosaic for every plane of interest), export
out
and compile them with another software. Does any of you have any
suggestion
of possible software that has the capability of compiling individual
planes
into a stack?

Please advise. Thank you!

Cheers,
Rachael Lim

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Rachaei-
I don't know where you are writing from, but you can do anything with
Advanced Visualization Systems software.  The learning curve is
pretty steep and they may not have it everywhere.

>  the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Hi! We are trying to run an experiment that requires image acquisition of a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed by
>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export out
>and compile them with another software. Does any of you have any suggestion
>of possible software that has the capability of compiling individual planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim

--
Carol A. Heckman, Ph.D.
Director, Center for Microscopy & Microanalysis
and Professor of Biological Sciences
Bowling Green State University
Bowling Green, OH 43403
USA
website: http://www.bgsu.edu/departments/biology/facilities/MnM

[George McNamara]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Rachel,

you may want to try out the software described in S.L. Wearne et al
2005 Neuroscience 136: 6610-680, http://www.mssm.edu/cnic/tools.html 
and http://www.mssm.edu/cnic/arborization.html (the latter is a web
summary of the paper). The process is done post acquisition.



At 03:57 AM 10/17/2007, you wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Hi! We are trying to run an experiment that requires image acquisition of a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed by
>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export out
>and compile them with another software. Does any of you have any suggestion
>of possible software that has the capability of compiling individual planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim

George McNamara, Ph.D.
University of Miami, Miller School of Medicine
Image Core
Miami, FL 33010
[hidden email]
[hidden email]
305-243-8436 office
http://home.earthlink.net/~pubspectra/
http://home.earthlink.net/~geomcnamara/
http://www.sylvester.org/health_pro/shared_resources/index.asp (see
Analytical Imaging Core Facility)

[Sven Terclavers]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Rachael,

I don't know if it's possible to install on your equipment, but I get nice
results with the Zeiss LSM510 software and their Multi Time 4.0 macro. Large
3D mosaics with multiple tracks (3 to 4 fluorophores) do not give problems,
unless the file is larger than 3Gb, but then it's not the software though
our Windows-version that blocks the use of more memory (a 64-bit system will
allow higher memory allocation, we run the 32-bit version).

It might be possible to create lsm-z-stack files from a z-stack saved as
single Tiff-files and then run the Mosaic tile-utility on those single
lsm-files, but this I've never tried.

Sven Terclavers

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Carol Heckman
Sent: Thursday, 18 October, 2007 01:36
To: [hidden email]
Subject: Re: [CONFOCAL] Mosaic with optical sectoning

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Rachaei-
I don't know where you are writing from, but you can do anything with
Advanced Visualization Systems software.  The learning curve is
pretty steep and they may not have it everywhere.

>  the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Hi! We are trying to run an experiment that requires image acquisition of a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed

by

>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export out
>and compile them with another software. Does any of you have any suggestion
>of possible software that has the capability of compiling individual planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim

--
Carol A. Heckman, Ph.D.
Director, Center for Microscopy & Microanalysis
and Professor of Biological Sciences
Bowling Green State University
Bowling Green, OH 43403
USA
website: http://www.bgsu.edu/departments/biology/facilities/MnM



Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

[Stanislav Vitha]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Hi Rachael,
you do not mention what instrument you are using; For multi-area time
lapse Z-stack data from our Olympus FV1000 confocal I have recently been
using the ImageJ mosaicking plug-in from the good people at NCMIR, which
can import the Olympus confocal files and also understands the XY mosaic
log file.

download at
http://www.ncmir.ucsd.edu/Software/imagej_mosaicking_plugins.htm

instructions at
http://www.ncmir.ucsd.edu/~skchow/rts2000/mosaicprocess.html

With our scope I set up acquisition of overlapping tiles (or for 3D,
overlapping z-stacks). The confocal software acquires the z-stacks and
also saves a log file with XY coordinates of each z-stack.

The mosaicking plugin reads the log file and based on the XY coordinates
of each tile assembles them into a mosaic. You end up with assembled
mosaic for each z-slice. Their file format is tiled tiff, which can be
read by some, but not all software.  


Stan Vitha

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

On Wed, 17 Oct 2007 15:57:07 +0800, Rachael Lim <[hidden email]>
wrote:

>Hi! We are trying to run an experiment that requires image acquisition of
a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed
by
>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export
out
>and compile them with another software. Does any of you have any
suggestion
>of possible software that has the capability of compiling individual
planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim
>=========================================================================

[Kevin Ryan-2]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Image-Pro, from Media Cybernetics, can assemble mosaics and stacks. Yes,
I'm biased; I write this software!

There are some limitations - due to Windows OS issues any _single_ frame
is limited to ~500MB (leaving room for operating on two images with an
output frame, plus the software, inside the ~1.6GB limit of Windows XP).
On a 64-bit system that goes up to ~700-900MB. If a single plane of your
mosaic is under that size limit Image-Pro can assemble your mosaics and
stacks for viewing.

If all individual frames are under the size limits Image-Pro will use
virtual memory to swap them in and out for operations. I've had >10GB of
images open at once, performing tracking on long time lapse series.

A mosaic with optical sectioning assembly would be a matter of:

(a) Tiling your mosaic images at a plane with good information, features
in all tiles of the mosaic,
(b) Applying that tiling to all planes, creating a series of mosaics,
and
(c) Viewing/measuring objects in your series of mosaics as a volume.

Note that Image-Pro can read most commonly available file formats. A
basic 3D viewer is included in the base Image-Pro; there is an
additional module for 3D object segmentation and analysis.

Kevin Ryan
Media Cybernetics, Inc.


> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
On
> Behalf Of Rachael Lim
> Sent: Wednesday, October 17, 2007 3:57 AM
> To: [hidden email]
> Subject: Mosaic with optical sectoning
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Hi! We are trying to run an experiment that requires image acquisition
of
> a
> very large area (a slice of rat brain; we use mosaic for this
purpose),
> along with optical sectioning.
>
> However, the software that we are currently using does not allow us to
> acquire both mosaic and optical sectioning simultaneously due to the
> extremely large file size produced (about 2GB), which cannot be
processed
> by
> the software (software limitation of file size is 200MB).
>
> I am wondering if it is possible for us to acquire the mosaic and
optical
> sectioning separately (i.e. mosaic for every plane of interest),
export

> out
> and compile them with another software. Does any of you have any
> suggestion
> of possible software that has the capability of compiling individual
> planes
> into a stack?
>
> Please advise. Thank you!
>
> Cheers,
> Rachael Lim

[Christian Götze]

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

COMMERCIAL WARNING!

Hi,

our company, arivis (http://www.arivis.com) provides the arivis Browser - a
software for handling very large image data. Using the Browser there is no
problem with the data size anymore. The software has its roots in confocal
applications and therefore should be suitable for your problem.
We support the acquisition by several devices directly, as Leica confocals
using LCS software, different cameras and stages or all TILL Photonics
devices. If your device is not supported you can import the single images
directly.

For getting an idea of the data size we work on usually look at
http://www.arivis.com/webview.

Don't hestitate to contact me for further questions.

Christian Goetze

On Wed, 17 Oct 2007 15:57:07 +0800, Rachael Lim <[hidden email]> wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Hi! We are trying to run an experiment that requires image acquisition of a
>very large area (a slice of rat brain; we use mosaic for this purpose),
>along with optical sectioning.
>
>However, the software that we are currently using does not allow us to
>acquire both mosaic and optical sectioning simultaneously due to the
>extremely large file size produced (about 2GB), which cannot be processed by
>the software (software limitation of file size is 200MB).
>
>I am wondering if it is possible for us to acquire the mosaic and optical
>sectioning separately (i.e. mosaic for every plane of interest), export out
>and compile them with another software. Does any of you have any suggestion
>of possible software that has the capability of compiling individual planes
>into a stack?
>
>Please advise. Thank you!
>
>Cheers,
>Rachael Lim
>=========================================================================