Re: ICS_opener release with Nikon C1 support

[Benjamin Abecassis]

Hi everyone,

I also have problems opening ids files which consist of stacks of images.
When i do import>ICS/IDS/sequence.ids it seems like it reads all the photos
(41 in the present case) and then opens two channels (one empty and one with
an actual image). The image does not look like the one i took at the
microscope. Anyway, i do not manage to get a single IDS file to be converted
into a stack or even to open just some of the 41 images.

Help would be welcome

Benjamin Abécassis
Post doctoral fellow
Laboratoire de Physique de la Matière Condensée et Nanostructures
Université de Lyon

[ctrueden]

Hi Benjamin,

I can't speak for the ICS_Opener plugin, but have you tried your data
with Bio-Formats (http://www.loci.wisc.edu/ome/formats.html)? If you
have and it does not work, we would be glad to look into it.

-Curtis

On 2/28/07, Benjamin Abecassis <[hidden email]> wrote:

> Hi everyone,
>
> I also have problems opening ids files which consist of stacks of images.
> When i do import>ICS/IDS/sequence.ids it seems like it reads all the photos
> (41 in the present case) and then opens two channels (one empty and one with
> an actual image). The image does not look like the one i took at the
> microscope. Anyway, i do not manage to get a single IDS file to be converted
> into a stack or even to open just some of the 41 images.
>
> Help would be welcome
>
> Benjamin Abécassis
> Post doctoral fellow
> Laboratoire de Physique de la Matière Condensée et Nanostructures
> Université de Lyon
>

[Nico Stuurman-4]

Hi Benjamin (and others),

I just updated the plugin (http://valelab.ucsf.edu/~nico/ijplugins/ 
Ics_Opener.html) with fixes for problems reported by Gerald Baron  
(not opening stacks saved in NIS Elements) and Jon Harman (not  
recognizing endianness and not opening filenames with the .ICS  
extension).  If this version does not fix your issues, please send me  
a (small) example file that you fail to open correctly.  I'll share  
those with Curtis (promised!).

I do expect that 8-bit interleaved files will not be opened  
correctly, but I'll need an example of such a file to fix it.

Hope this helps,

Nico


On Feb 28, 2007, at 10:47 AM, Benjamin Abecassis wrote:

> Hi everyone,
>
> I also have problems opening ids files which consist of stacks of  
> images.
> When i do import>ICS/IDS/sequence.ids it seems like it reads all  
> the photos
> (41 in the present case) and then opens two channels (one empty and  
> one with
> an actual image). The image does not look like the one i took at the
> microscope. Anyway, i do not manage to get a single IDS file to be  
> converted
> into a stack or even to open just some of the 41 images.
>
> Help would be welcome
>
> Benjamin Abécassis
> Post doctoral fellow
> Laboratoire de Physique de la Matière Condensée et Nanostructures
> Université de Lyon

[Benjamin Abecassis]

It works fine with the new plugin.
One question two good answers in just one day !
Thanks a lot.

Regards

Benjamin

2007/3/1, Nico Stuurman <[hidden email]>:

>
> Hi Benjamin (and others),
>
> I just updated the plugin (http://valelab.ucsf.edu/~nico/ijplugins/
> Ics_Opener.html) with fixes for problems reported by Gerald Baron
> (not opening stacks saved in NIS Elements) and Jon Harman (not
> recognizing endianness and not opening filenames with the .ICS
> extension).  If this version does not fix your issues, please send me
> a (small) example file that you fail to open correctly.  I'll share
> those with Curtis (promised!).
>
> I do expect that 8-bit interleaved files will not be opened
> correctly, but I'll need an example of such a file to fix it.
>
> Hope this helps,
>
> Nico
>
>
> On Feb 28, 2007, at 10:47 AM, Benjamin Abecassis wrote:
>
> > Hi everyone,
> >
> > I also have problems opening ids files which consist of stacks of
> > images.
> > When i do import>ICS/IDS/sequence.ids it seems like it reads all
> > the photos
> > (41 in the present case) and then opens two channels (one empty and
> > one with
> > an actual image). The image does not look like the one i took at the
> > microscope. Anyway, i do not manage to get a single IDS file to be
> > converted
> > into a stack or even to open just some of the 41 images.
> >
> > Help would be welcome
> >
> > Benjamin Abécassis
> > Post doctoral fellow
> > Laboratoire de Physique de la Matière Condensée et Nanostructures
> > Université de Lyon
>