Image Explorer

[simon walker (BI)]

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

Dear Confocalists,

For many reasons it seemed to me a good idea to create an image explorer
program (like Windows Explorer) that would allow you to see thumbnail images
of proprietary confocal file formats, in addition to standard image file formats.  
I suggested the idea to one of our Bioinformtics guys and he's written a
program which he's called FocalPoint.  At this point you may well tell me this is
reinventing the wheel, but to date, I haven't seen anything quite like this.

The program displays thumbnail images of Zeiss (.lsm) and Olympus (.oib, .oif)
confocal images files in addition to standard image file formats (avi, jpg, tiff,
bmp, png).  If the image file contains multiple channels or images acquired
over depth or time then slider bars appear adjacent to the thumbnail image
and allow you to navigate through the stack.  You can also easily resize the
thumbnail images to allow you to see more or less detail as required.

If there are people out there who think they may benefit from this software
then it can be freely downloaded here (PC and Mac):
http://www.bioinformatics.bbsrc.ac.uk/projects/focalpoint/

At the moment the software is still work in progress so there may be one or
two bugs.  Let me know if you find anything.  I'd also be interested to hear if
anyone has any suggestions on how the software could be improved.  
Currently there is support only for Zeiss and Olympus confocal file formats as
these are the instruments we have here.  If anyone would like support added
for other common confocal file formats (eg .lei) then perhaps you could send
me a few small sample files and we'll see what we can do.

Simon Walker
Babraham Institute
Cambridge
UK
CB22 3AT

[lechristophe]

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal I only have one request : would it be possible to support .stk Metamorph stacks (built-in in ImageJ) and .lei/.lif leica files (by using the LOCI tools importer API) ?

Christophe

On Mon, Apr 21, 2008 at 11:17 AM, Simon Walker <[hidden email]> wrote:

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

Dear Confocalists,

For many reasons it seemed to me a good idea to create an image explorer
program (like Windows Explorer) that would allow you to see thumbnail images
of proprietary confocal file formats, in addition to standard image file formats.
I suggested the idea to one of our Bioinformtics guys and he's written a
program which he's called FocalPoint.  At this point you may well tell me this is
reinventing the wheel, but to date, I haven't seen anything quite like this.

The program displays thumbnail images of Zeiss (.lsm) and Olympus (.oib, .oif)
confocal images files in addition to standard image file formats (avi, jpg, tiff,
bmp, png).  If the image file contains multiple channels or images acquired
over depth or time then slider bars appear adjacent to the thumbnail image
and allow you to navigate through the stack.  You can also easily resize the
thumbnail images to allow you to see more or less detail as required.

If there are people out there who think they may benefit from this software
then it can be freely downloaded here (PC and Mac):
http://www.bioinformatics.bbsrc.ac.uk/projects/focalpoint/

At the moment the software is still work in progress so there may be one or
two bugs.  Let me know if you find anything.  I'd also be interested to hear if
anyone has any suggestions on how the software could be improved.
Currently there is support only for Zeiss and Olympus confocal file formats as
these are the instruments we have here.  If anyone would like support added
for other common confocal file formats (eg .lei) then perhaps you could send
me a few small sample files and we'll see what we can do.

Simon Walker
Babraham Institute
Cambridge
UK
CB22 3AT

[John Runions]

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

Dear Simon, this will be a welcome bit of software. I will download it and try it out.  Before becoming a Zeiss user, I would catalogue all of my image files into subject specific libraries using Portfolio or comparable software.  Various other software handle the Zeiss file format, e.g. Where Is It, but still require a saved separate image to be catalogued for image stacks and time series (correct me if I'm wrong - I usually am). An image organising program very quickly becomes cumbersome if every image from a stack or timeseries is thumbnailed individually.   Sliders for navigating through stacks sounds like a perfect solution.  Have your colleague keep up the good work.  Regards, John.

Simon Walker wrote:

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

Dear Confocalists,

For many reasons it seemed to me a good idea to create an image explorer 
program (like Windows Explorer) that would allow you to see thumbnail images 
of proprietary confocal file formats, in addition to standard image file formats.  
I suggested the idea to one of our Bioinformtics guys and he's written a 
program which he's called FocalPoint.  At this point you may well tell me this is 
reinventing the wheel, but to date, I haven't seen anything quite like this.

The program displays thumbnail images of Zeiss (.lsm) and Olympus (.oib, .oif) 
confocal images files in addition to standard image file formats (avi, jpg, tiff, 
bmp, png).  If the image file contains multiple channels or images acquired 
over depth or time then slider bars appear adjacent to the thumbnail image 
and allow you to navigate through the stack.  You can also easily resize the 
thumbnail images to allow you to see more or less detail as required.

If there are people out there who think they may benefit from this software 
then it can be freely downloaded here (PC and Mac):
http://www.bioinformatics.bbsrc.ac.uk/projects/focalpoint/

At the moment the software is still work in progress so there may be one or 
two bugs.  Let me know if you find anything.  I'd also be interested to hear if 
anyone has any suggestions on how the software could be improved.  
Currently there is support only for Zeiss and Olympus confocal file formats as 
these are the instruments we have here.  If anyone would like support added 
for other common confocal file formats (eg .lei) then perhaps you could send 
me a few small sample files and we'll see what we can do.

Simon Walker
Babraham Institute
Cambridge
UK
CB22 3AT
  

[Kevin W Eliceiri]

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

We are very interested in having additional applications utilize the Bio-formats library (http://www.loci.wisc.edu/ome/formats.html). By doing so your application would support the 55 plus formats that Bio-formats can currently open. If you are interested in doing this, please contact us offlist and we can help.

best,
kevin

Kevin W. Eliceiri
Director
Laboratory for Optical and Computational Instrumentation
http://www.loci.wisc.edu
Room 271 Animal Sciences
1675 Observatory Drive
Madison, WI 53706
Phone: [phone]
Fax: [phone]

----- Original Message -----
From: Christophe Leterrier <[hidden email]>
Date: Tuesday, April 22, 2008 2:24 am
Subject: Re: Image Explorer
To: [hidden email]

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> I only have one request : would it be possible to support .stk Metamorph
> stacks (built-in in ImageJ) and .lei/.lif leica files (by using the LOCI
> tools importer API) ?
>
> Christophe
>
> On Mon, Apr 21, 2008 at 11:17 AM, Simon Walker <[hidden email]>
> wrote:
>
> > Search the CONFOCAL archive at
> > http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
> >
> > Dear Confocalists,
> >
> > For many reasons it seemed to me a good idea to create an image explorer
> > program (like Windows Explorer) that would allow you to see thumbnail
> > images
> > of proprietary confocal file formats, in addition to standard image
> file
> > formats.
> > I suggested the idea to one of our Bioinformtics guys and he's
> written a
> > program which he's called FocalPoint.  At this point you may well
> tell me
> > this is
> > reinventing the wheel, but to date, I haven't seen anything quite like
> > this.
> >
> > The program displays thumbnail images of Zeiss (.lsm) and Olympus (.oib,
> > .oif)
> > confocal images files in addition to standard image file formats (avi,
> > jpg, tiff,
> > bmp, png).  If the image file contains multiple channels or images
> > acquired
> > over depth or time then slider bars appear adjacent to the thumbnail
> image
> > and allow you to navigate through the stack.  You can also easily resize
> > the
> > thumbnail images to allow you to see more or less detail as required.
> >
> > If there are people out there who think they may benefit from this
> > software
> > then it can be freely downloaded here (PC and Mac):
> > http://www.bioinformatics.bbsrc.ac.uk/projects/focalpoint/
> >
> > At the moment the software is still work in progress so there may be
> one
> > or
> > two bugs.  Let me know if you find anything.  I'd also be interested
> to
> > hear if
> > anyone has any suggestions on how the software could be improved.
> > Currently there is support only for Zeiss and Olympus confocal file
> > formats as
> > these are the instruments we have here.  If anyone would like support
> > added
> > for other common confocal file formats (eg .lei) then perhaps you could
> > send
> > me a few small sample files and we'll see what we can do.
> >
> > Simon Walker
> > Babraham Institute
> > Cambridge
> > UK
> > CB22 3AT
> >