ICS_opener release with Nikon C1 support

[Nico Stuurman-2]

Rudolf Oldenbourg send me his java code to de-interleave files opened  
with ICS_Opener.  I added his code to the ICS opener plugin, which  
now should automatically recognize whether a file is deinterleaved  
and the plugin opened the few NIkon C1 images I had quite nicely.  I  
haven't had time to test it extensively (I don't have a C1; actually,  
I no longer work with ICS files at all), so please give it a try and  
let me know if there are problems.  Download at: http://
valelab.ucsf.edu/~nico/ijplugins/Ics_Opener.html

All praise for the Nikon support goes to Rudolf, I'll take complaints  
and bug reports.

B.t.w., Chris, I didn't follow matters closely, so maybe the  
BioFormats plugin already opens the Nikon C1 ICS files?

Best,


Nico Stuurman
Vale Lab, UCSF MC2240
HHMI / Dept. of Cellular and Molecular Pharmacology
University of California, San Francisco
Genentech Hall, Room N316
600 16th street
San Francisco, CA 94158-2517

[ctrueden]

Hi Nico,

I do not believe we have any Nikon C1 ICS files, so it is unlikely
that Bio-Formats supports them. But feel free to give it a try. If
they don't work, we would be glad to look into adding support if you
could send us some sample data. I'm sure your updated ICS_Opener
plugin would be a good resource, as well.

Thanks,
Curtis

On 2/16/07, Nico Stuurman <[hidden email]> wrote:

> Rudolf Oldenbourg send me his java code to de-interleave files opened
> with ICS_Opener.  I added his code to the ICS opener plugin, which
> now should automatically recognize whether a file is deinterleaved
> and the plugin opened the few NIkon C1 images I had quite nicely.  I
> haven't had time to test it extensively (I don't have a C1; actually,
> I no longer work with ICS files at all), so please give it a try and
> let me know if there are problems.  Download at: http://
> valelab.ucsf.edu/~nico/ijplugins/Ics_Opener.html
>
> All praise for the Nikon support goes to Rudolf, I'll take complaints
> and bug reports.
>
> B.t.w., Chris, I didn't follow matters closely, so maybe the
> BioFormats plugin already opens the Nikon C1 ICS files?
>
> Best,
>
>
> Nico Stuurman
> Vale Lab, UCSF MC2240
> HHMI / Dept. of Cellular and Molecular Pharmacology
> University of California, San Francisco
> Genentech Hall, Room N316
> 600 16th street
> San Francisco, CA 94158-2517
>

[Perry, Griffin M]

Couldn't open interleaved .ids stacks.  *shrugs*

With the "old" ICS opener version, I just did File->Import->Image
Sequence and open up one .ids and all of them opened just fine.  The
only up-side to having a deinterleaving ics opener plugin is to cut down
on files (especially for spectral).  When saved, there are 8 files
(ics/ids for our 3 channels, an extra .ics and a .isr that puts them
back together in NotSo-EZC1) versus 2 files in an interleaved file.  4x
the amount of files written to disk, so I guess it could help fragment
hard drives.

I'm currently using EZ-C1 3.2 Build 610.  I need to update to EZ-C1
3.30.

Griffin Perry
Research Assistant
Department of Endodontics, Dental School
University of Texas Health Science Center
7703 Floyd Curl Drive Mail Code 7892
San Antonio, TX 78229-3900
Lab: [phone] FAX [phone]
E-mail: [hidden email]

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Curtis Rueden
Sent: Friday, February 16, 2007 12:19 PM
To: [hidden email]
Subject: Re: ICS_opener release with Nikon C1 support

Hi Nico,

I do not believe we have any Nikon C1 ICS files, so it is unlikely
that Bio-Formats supports them. But feel free to give it a try. If
they don't work, we would be glad to look into adding support if you
could send us some sample data. I'm sure your updated ICS_Opener
plugin would be a good resource, as well.

Thanks,
Curtis

On 2/16/07, Nico Stuurman <[hidden email]> wrote:

> Rudolf Oldenbourg send me his java code to de-interleave files opened
> with ICS_Opener.  I added his code to the ICS opener plugin, which
> now should automatically recognize whether a file is deinterleaved
> and the plugin opened the few NIkon C1 images I had quite nicely.  I
> haven't had time to test it extensively (I don't have a C1; actually,
> I no longer work with ICS files at all), so please give it a try and
> let me know if there are problems.  Download at: http://
> valelab.ucsf.edu/~nico/ijplugins/Ics_Opener.html
>
> All praise for the Nikon support goes to Rudolf, I'll take complaints
> and bug reports.
>
> B.t.w., Chris, I didn't follow matters closely, so maybe the
> BioFormats plugin already opens the Nikon C1 ICS files?
>
> Best,
>
>
> Nico Stuurman
> Vale Lab, UCSF MC2240
> HHMI / Dept. of Cellular and Molecular Pharmacology
> University of California, San Francisco
> Genentech Hall, Room N316
> 600 16th street
> San Francisco, CA 94158-2517
>

[Nico Stuurman-2]

> Couldn't open interleaved .ids stacks.  *shrugs*

Instead of shrugging you could:
1. Use the included source code to fix the problem and submit the fix  
to the plugin's author
2. Send a comprehensible bug report to the plugin's author (including  
a small example of the problematic files).
Option #2 has gotten a bit harder since shrugging leads to automatic  
addition of your email address to my spam filters.

Nico

> With the "old" ICS opener version, I just did File->Import->Image
> Sequence and open up one .ids and all of them opened just fine.  The
> only up-side to having a deinterleaving ics opener plugin is to cut  
> down
> on files (especially for spectral).  When saved, there are 8 files
> (ics/ids for our 3 channels, an extra .ics and a .isr that puts them
> back together in NotSo-EZC1) versus 2 files in an interleaved  
> file.  4x
> the amount of files written to disk, so I guess it could help fragment
> hard drives.
>
> I'm currently using EZ-C1 3.2 Build 610.  I need to update to EZ-C1
> 3.30.
>
> Griffin Perry
> Research Assistant
> Department of Endodontics, Dental School
> University of Texas Health Science Center
> 7703 Floyd Curl Drive Mail Code 7892
> San Antonio, TX 78229-3900
> Lab: [phone] FAX [phone]
> E-mail: [hidden email]
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Curtis Rueden
> Sent: Friday, February 16, 2007 12:19 PM
> To: [hidden email]
> Subject: Re: ICS_opener release with Nikon C1 support
>
> Hi Nico,
>
> I do not believe we have any Nikon C1 ICS files, so it is unlikely
> that Bio-Formats supports them. But feel free to give it a try. If
> they don't work, we would be glad to look into adding support if you
> could send us some sample data. I'm sure your updated ICS_Opener
> plugin would be a good resource, as well.
>
> Thanks,
> Curtis
>
> On 2/16/07, Nico Stuurman <[hidden email]> wrote:
>> Rudolf Oldenbourg send me his java code to de-interleave files opened
>> with ICS_Opener.  I added his code to the ICS opener plugin, which
>> now should automatically recognize whether a file is deinterleaved
>> and the plugin opened the few NIkon C1 images I had quite nicely.  I
>> haven't had time to test it extensively (I don't have a C1; actually,
>> I no longer work with ICS files at all), so please give it a try and
>> let me know if there are problems.  Download at: http://
>> valelab.ucsf.edu/~nico/ijplugins/Ics_Opener.html
>>
>> All praise for the Nikon support goes to Rudolf, I'll take complaints
>> and bug reports.
>>
>> B.t.w., Chris, I didn't follow matters closely, so maybe the
>> BioFormats plugin already opens the Nikon C1 ICS files?
>>
>> Best,
>>
>>
>> Nico Stuurman
>> Vale Lab, UCSF MC2240
>> HHMI / Dept. of Cellular and Molecular Pharmacology
>> University of California, San Francisco
>> Genentech Hall, Room N316
>> 600 16th street
>> San Francisco, CA 94158-2517
>>