CellR and ImageJ

[Maria Luisa Malosio]

Dear ImageJ community
I have problems with image files generated with the Olympus proprietary software "CellR".
I would like to know if there is a way to open apl files from ImageJ and also to open the tif
files generated by CellR without trasnforming them into the 8-bit format.
Thank you very much in advance
Sincerely
Marialuisa Malosio

Maria Luisa Malosio, PhD
Diabetes Research Institute
Cell Imaging Unit
L25, 1°piano, Settore Q
Fondazione Centro San Raffaele del Monte Tabor
Via Olgettina 60
20132 Milano
Italy
Phone:[phone] or 2913
Fax:  [phone]
Cell 3471656237

[ctrueden]

Hi Maria,

Bio-Formats (http://www.loci.wisc.edu/ome/formats-imagej.html) has
preliminary support for the Olympus CellR/APL format. Give it a try and let
us know if you run into any trouble. We'd also be interested in hearing
whether it works with the TIFF files from CellR (no reason it shouldn't).

Cheers,
Curtis

On Wed, Oct 8, 2008 at 2:29 AM, Maria Luisa Malosio <
[hidden email]> wrote:

> Dear ImageJ community
> I have problems with image files generated with the Olympus proprietary
> software "CellR".
> I would like to know if there is a way to open apl files from ImageJ and
> also to open the tif
> files generated by CellR without trasnforming them into the 8-bit format.
> Thank you very much in advance
> Sincerely
> Marialuisa Malosio
>
> Maria Luisa Malosio, PhD
> Diabetes Research Institute
> Cell Imaging Unit
> L25, 1°piano, Settore Q
> Fondazione Centro San Raffaele del Monte Tabor
> Via Olgettina 60
> 20132 Milano
> Italy
> Phone:[phone] or 2913
> Fax:  [phone]
> Cell 3471656237
>

[Maria Luisa Malosio]

Dear Curtis,
Many thanks for your suggestion.
I have added the Loci_tools plugin to ImageJ.
I have  tried to open an uncompressed  tiff file generated by CellR using
the Bio-format importer, is this correct? I was able to open it and the two
channels of the acquisition were visible in tow separate windows, though
with different false colors than originally. I have also tried to measure
the signal intensity of some ROIs, that I had already analyzed with CellR.
The problem I see at the moment are the numbers that I obtain from these
measurements, they are quite different from those that I obtained within
CellR. The range of CellR is 1000-1300 for an average ROI, in ImageJ I
obtain values of 17000-35000 for the same type of ROIs. Also the background
value is higher than a ROI around a signal. This is scary!!! Don't you think
so? I don't know exactly what to do in order to trust the analysis on the
original files opened in ImageJ.
Thanks for any imput.
Sincerely
Marialuisa

Dr. Maria Luisa Malosio, PhD
Diabetes Research Institute
Cell Imaging Unit
San Raffaele Scientific Institute
Via Olgettina 60
20132 Milano
Italy
Phone:[phone] or 2913
Fax:  [phone]
Cell 3471656237

P Please consider the environment before printing this email

> From: Curtis Rueden <[hidden email]>
> Reply-To: ImageJ Interest Group <[hidden email]>
> Date: Wed, 8 Oct 2008 11:19:48 -0500
> To: "[hidden email]"
> Subject: Re: CellR and ImageJ
>
> Hi Maria,
>
> Bio-Formats (http://www.loci.wisc.edu/ome/formats-imagej.html) has
> preliminary support for the Olympus CellR/APL format. Give it a try and let
> us know if you run into any trouble. We'd also be interested in hearing
> whether it works with the TIFF files from CellR (no reason it shouldn't).
>
> Cheers,
> Curtis
>
> On Wed, Oct 8, 2008 at 2:29 AM, Maria Luisa Malosio <
> [hidden email]> wrote:
>
>> Dear ImageJ community
>> I have problems with image files generated with the Olympus proprietary
>> software "CellR".
>> I would like to know if there is a way to open apl files from ImageJ and
>> also to open the tif
>> files generated by CellR without trasnforming them into the 8-bit format.
>> Thank you very much in advance
>> Sincerely
>> Marialuisa Malosio
>>
>> Maria Luisa Malosio, PhD
>> Diabetes Research Institute
>> Cell Imaging Unit
>> L25, 1°piano, Settore Q
>> Fondazione Centro San Raffaele del Monte Tabor
>> Via Olgettina 60
>> 20132 Milano
>> Italy
>> Phone:[phone] or 2913
>> Fax:  [phone]
>> Cell 3471656237
>>

[Arne Seitz-2]

Dear Marialuisa,

the numbers you get are less scary if you take the different bit-depth into
account. If you have a 12-bit camera on your system everything is more or
less fine. For the 12-bit image you get 1000/4096=0.24 equals 24% of dynamic
range. As ImageJ is not supporting 12-bit everything is converted to 16-bit.
If you do the same calculation as above you get: 17000/65536=0.26. Thus the
values are more or less identical if you take the dynamic range into
account.

Cheers Arne


____________________________________________________
 
Dr. Arne Seitz, Scientific Officer
Advanced Light Microscopy Facility
EMBL Heidelberg
 
[phone]

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von
marialuisa malosio
Gesendet: Freitag, 10. Oktober 2008 11:32
An: [hidden email]
Betreff: Re: CellR and ImageJ
Wichtigkeit: Hoch

Dear Curtis,
Many thanks for your suggestion.
I have added the Loci_tools plugin to ImageJ.
I have  tried to open an uncompressed  tiff file generated by CellR using
the Bio-format importer, is this correct? I was able to open it and the two
channels of the acquisition were visible in tow separate windows, though
with different false colors than originally. I have also tried to measure
the signal intensity of some ROIs, that I had already analyzed with CellR.
The problem I see at the moment are the numbers that I obtain from these
measurements, they are quite different from those that I obtained within
CellR. The range of CellR is 1000-1300 for an average ROI, in ImageJ I
obtain values of 17000-35000 for the same type of ROIs. Also the background
value is higher than a ROI around a signal. This is scary!!! Don't you think
so? I don't know exactly what to do in order to trust the analysis on the
original files opened in ImageJ.
Thanks for any imput.
Sincerely
Marialuisa

Dr. Maria Luisa Malosio, PhD
Diabetes Research Institute
Cell Imaging Unit
San Raffaele Scientific Institute
Via Olgettina 60
20132 Milano
Italy
Phone:[phone] or 2913
Fax:  [phone]
Cell 3471656237

P Please consider the environment before printing this email

> From: Curtis Rueden <[hidden email]>
> Reply-To: ImageJ Interest Group <[hidden email]>
> Date: Wed, 8 Oct 2008 11:19:48 -0500
> To: "[hidden email]"
> Subject: Re: CellR and ImageJ
>
> Hi Maria,
>
> Bio-Formats (http://www.loci.wisc.edu/ome/formats-imagej.html) has
> preliminary support for the Olympus CellR/APL format. Give it a try and

let

> us know if you run into any trouble. We'd also be interested in hearing
> whether it works with the TIFF files from CellR (no reason it shouldn't).
>
> Cheers,
> Curtis
>
> On Wed, Oct 8, 2008 at 2:29 AM, Maria Luisa Malosio <
> [hidden email]> wrote:
>
>> Dear ImageJ community
>> I have problems with image files generated with the Olympus proprietary
>> software "CellR".
>> I would like to know if there is a way to open apl files from ImageJ and
>> also to open the tif
>> files generated by CellR without trasnforming them into the 8-bit format.
>> Thank you very much in advance
>> Sincerely
>> Marialuisa Malosio
>>
>> Maria Luisa Malosio, PhD
>> Diabetes Research Institute
>> Cell Imaging Unit
>> L25, 1°piano, Settore Q
>> Fondazione Centro San Raffaele del Monte Tabor
>> Via Olgettina 60
>> 20132 Milano
>> Italy
>> Phone:[phone] or 2913
>> Fax:  [phone]
>> Cell 3471656237
>>

[Mathieu Marchand-2]

> As ImageJ is not supporting 12-bit everything is converted to 16-bit.

I don't think so
ImageJ opens 12 bits images as 16bits, but it does NOT change intensity values.
a 12bits image in imageJ will be a 16bits image with no value higher
than 4095 (the max for 12bits).

When you are saving your 16bits tiff files in cellR, maybe you are
choosing an option where cellR stretch the intensity values over the
full 16bit range (0-65k) so it looks good in Photoshop?
If not, it could be an issue with bio-formats.

--
Mathieu Marchand
--
Bio-Imaging Resource Center, The Rockefeller University
1230 York Avenue, box 209, New York, NY 10021
http://www.rockefeller.edu/bioimaging .
[phone] (7489 for fax)

> Dear Marialuisa,
>
> the numbers you get are less scary if you take the different bit-depth into
> account. If you have a 12-bit camera on your system everything is more or
> less fine. For the 12-bit image you get 1000/4096=0.24 equals 24% of dynamic
> range. As ImageJ is not supporting 12-bit everything is converted to 16-bit.
> If you do the same calculation as above you get: 17000/65536=0.26. Thus the
> values are more or less identical if you take the dynamic range into
> account.
>
> Cheers Arne
>
>
> ____________________________________________________
>
> Dr. Arne Seitz, Scientific Officer
> Advanced Light Microscopy Facility
> EMBL Heidelberg
>
> [phone]
>
> -----Ursprüngliche Nachricht-----
> Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von
> marialuisa malosio
> Gesendet: Freitag, 10. Oktober 2008 11:32
> An: [hidden email]
> Betreff: Re: CellR and ImageJ
> Wichtigkeit: Hoch
>
> Dear Curtis,
> Many thanks for your suggestion.
> I have added the Loci_tools plugin to ImageJ.
> I have  tried to open an uncompressed  tiff file generated by CellR using
> the Bio-format importer, is this correct? I was able to open it and the two
> channels of the acquisition were visible in tow separate windows, though
> with different false colors than originally. I have also tried to measure
> the signal intensity of some ROIs, that I had already analyzed with CellR.
> The problem I see at the moment are the numbers that I obtain from these
> measurements, they are quite different from those that I obtained within
> CellR. The range of CellR is 1000-1300 for an average ROI, in ImageJ I
> obtain values of 17000-35000 for the same type of ROIs. Also the background
> value is higher than a ROI around a signal. This is scary!!! Don't you think
> so? I don't know exactly what to do in order to trust the analysis on the
> original files opened in ImageJ.
> Thanks for any imput.
> Sincerely
> Marialuisa
>
> Dr. Maria Luisa Malosio, PhD
> Diabetes Research Institute
> Cell Imaging Unit
> San Raffaele Scientific Institute
> Via Olgettina 60
> 20132 Milano
> Italy
> Phone:[phone] or 2913
> Fax:  [phone]
> Cell 3471656237
>
> P Please consider the environment before printing this email
>
>
>> From: Curtis Rueden <[hidden email]>
>> Reply-To: ImageJ Interest Group <[hidden email]>
>> Date: Wed, 8 Oct 2008 11:19:48 -0500
>> To: "[hidden email]"
>> Subject: Re: CellR and ImageJ
>>
>> Hi Maria,
>>
>> Bio-Formats (http://www.loci.wisc.edu/ome/formats-imagej.html) has
>> preliminary support for the Olympus CellR/APL format. Give it a try and
> let
>> us know if you run into any trouble. We'd also be interested in hearing
>> whether it works with the TIFF files from CellR (no reason it shouldn't).
>>
>> Cheers,
>> Curtis
>>
>> On Wed, Oct 8, 2008 at 2:29 AM, Maria Luisa Malosio <
>> [hidden email]> wrote:
>>
>>> Dear ImageJ community
>>> I have problems with image files generated with the Olympus proprietary
>>> software "CellR".
>>> I would like to know if there is a way to open apl files from ImageJ and
>>> also to open the tif
>>> files generated by CellR without trasnforming them into the 8-bit format.
>>> Thank you very much in advance
>>> Sincerely
>>> Marialuisa Malosio
>>>
>>> Maria Luisa Malosio, PhD
>>> Diabetes Research Institute
>>> Cell Imaging Unit
>>> L25, 1°piano, Settore Q
>>> Fondazione Centro San Raffaele del Monte Tabor
>>> Via Olgettina 60
>>> 20132 Milano
>>> Italy
>>> Phone:[phone] or 2913
>>> Fax:  [phone]
>>> Cell 3471656237
>>>
>

[ctrueden]

Hi Marialuisa,

Many thanks for your suggestion.
> I have added the Loci_tools plugin to ImageJ.
> I have  tried to open an uncompressed  tiff file generated by CellR using
> the Bio-format importer, is this correct?


With Bio-Formats, you can open either the original APL file or the exported
uncompressed TIFF. Use whichever one is easier for you. If you notice
problems with either approach, please let us know, as we are committed to
fixing any bugs in the Bio-Formats library.

I was able to open it and the two

> channels of the acquisition were visible in tow separate windows, though
> with different false colors than originally. I have also tried to measure
> the signal intensity of some ROIs, that I had already analyzed with CellR.
> The problem I see at the moment are the numbers that I obtain from these
> measurements, they are quite different from those that I obtained within
> CellR. The range of CellR is 1000-1300 for an average ROI, in ImageJ I
> obtain values of 17000-35000 for the same type of ROIs. Also the background
> value is higher than a ROI around a signal. This is scary!!! Don't you
> think
> so? I don't know exactly what to do in order to trust the analysis on the
> original files opened in ImageJ.
>

I do not know whether this is a problem with Bio-Formats. Would you be able
to send us both the original APL, and corresponding exported TIFF, for one
of your datasets? It would be very helpful for investigating the problem,
and we would use the data only for internal development purposes. Files
under 15 MB can be sent as email attachments; if you need somewhere to store
larger files, let me know and I will send you our FTP server information
off-list.

Thanks,
Curtis

On Fri, Oct 10, 2008 at 4:31 AM, marialuisa malosio <
[hidden email]> wrote:

> Dear Curtis,
> Many thanks for your suggestion.
> I have added the Loci_tools plugin to ImageJ.
> I have  tried to open an uncompressed  tiff file generated by CellR using
> the Bio-format importer, is this correct? I was able to open it and the two
> channels of the acquisition were visible in tow separate windows, though
> with different false colors than originally. I have also tried to measure
> the signal intensity of some ROIs, that I had already analyzed with CellR.
> The problem I see at the moment are the numbers that I obtain from these
> measurements, they are quite different from those that I obtained within
> CellR. The range of CellR is 1000-1300 for an average ROI, in ImageJ I
> obtain values of 17000-35000 for the same type of ROIs. Also the background
> value is higher than a ROI around a signal. This is scary!!! Don't you
> think
> so? I don't know exactly what to do in order to trust the analysis on the
> original files opened in ImageJ.
> Thanks for any imput.
> Sincerely
> Marialuisa
>
> Dr. Maria Luisa Malosio, PhD
> Diabetes Research Institute
> Cell Imaging Unit
> San Raffaele Scientific Institute
> Via Olgettina 60
> 20132 Milano
> Italy
> Phone:[phone] or 2913
> Fax:  [phone]
> Cell 3471656237
>
> P Please consider the environment before printing this email
>
>
> > From: Curtis Rueden <[hidden email]>
> > Reply-To: ImageJ Interest Group <[hidden email]>
> > Date: Wed, 8 Oct 2008 11:19:48 -0500
> > To: "[hidden email]"
> > Subject: Re: CellR and ImageJ
> >
> > Hi Maria,
> >
> > Bio-Formats (http://www.loci.wisc.edu/ome/formats-imagej.html) has
> > preliminary support for the Olympus CellR/APL format. Give it a try and
> let
> > us know if you run into any trouble. We'd also be interested in hearing
> > whether it works with the TIFF files from CellR (no reason it shouldn't).
> >
> > Cheers,
> > Curtis
> >
> > On Wed, Oct 8, 2008 at 2:29 AM, Maria Luisa Malosio <
> > [hidden email]> wrote:
> >
> >> Dear ImageJ community
> >> I have problems with image files generated with the Olympus proprietary
> >> software "CellR".
> >> I would like to know if there is a way to open apl files from ImageJ and
> >> also to open the tif
> >> files generated by CellR without trasnforming them into the 8-bit
> format.
> >> Thank you very much in advance
> >> Sincerely
> >> Marialuisa Malosio
> >>
> >> Maria Luisa Malosio, PhD
> >> Diabetes Research Institute
> >> Cell Imaging Unit
> >> L25, 1°piano, Settore Q
> >> Fondazione Centro San Raffaele del Monte Tabor
> >> Via Olgettina 60
> >> 20132 Milano
> >> Italy
> >> Phone:[phone] or 2913
> >> Fax:  [phone]
> >> Cell 3471656237
> >>
>