Zeiss LSM images and LOCI Bio-Formats library

[Markus Böttcher]

Hi...

I have always used the LOCI-plugin to work with my images I acquired in
the Zeiss LSM format.
Since the last ImageJ-update only a small number of images in the *.mdb
archive  is accessible by the LOCI-plugin.
Does anyone know how to solve that problem?

thanks and
best regards,
Markus

[dscho]

Hi,

On Mon, 15 Feb 2010, Markus Böttcher wrote:

> I have always used the LOCI-plugin to work with my images I acquired in the
> Zeiss LSM format.
> Since the last ImageJ-update only a small number of images in the *.mdb
> archive  is accessible by the LOCI-plugin.

There was an important change how .lsm files > 2GB are read, that is the
only change I can think of quickly.

> Does anyone know how to solve that problem?

If you would grace us with a description how this fails, it might be
easier for those volunteering to help you.

Ciao,
Dscho

[Melissa Linkert-2]

Hi Markus,

> I have always used the LOCI-plugin to work with my images I acquired in the
> Zeiss LSM format.
> Since the last ImageJ-update only a small number of images in the *.mdb
> archive  is accessible by the LOCI-plugin.

There was a bug in the 4.1.0 release of Bio-Formats that sounds very
similar to the problem that you describe; however, this bug was fixed
in the latest (4.1.1) release.  As it's not clear which version of
Bio-Formats you are using, could you please make sure that you are
using the 4.1.1 release?  The version number can be found by selecting
"Help > About Plugins > LOCI Plugins".

If the problem occurs with 4.1.1, then as Johannes mentioned, it would
be very helpful if you could provide a more complete description of
the problem.  In particular, it would be helpful if you could send any
error messages that you see.

Regards,
-Melissa

On Mon, Feb 15, 2010 at 2:56 AM, Markus Böttcher
<[hidden email]> wrote:

> Hi...
>
> I have always used the LOCI-plugin to work with my images I acquired in the
> Zeiss LSM format.
> Since the last ImageJ-update only a small number of images in the *.mdb
> archive  is accessible by the LOCI-plugin.
> Does anyone know how to solve that problem?
>
> thanks and
> best regards,
> Markus
>

[Markus Böttcher]

Hi Melissa,

The latest stable release (built 3rd dec 2009, revision 5727) and ImageJ
1.43q are installed on my computer...
I'm sorry that I can't send any error messages because there are no
error messages.
Starting the loci-plugin as:
plugins -> loci -> databrowser -> selecting the *.mdb file
results in an overview of only a small number of images that are
included in the *.mdb archive...

best regards,
Markus

PS.:
I'm new to the mailing list and would like to say that I'm glad that
there are lot people trying to help each other... thanks a lot...

Am 15.02.2010 21:51, schrieb Melissa Linkert:

> Hi Markus,
>
>    
>> I have always used the LOCI-plugin to work with my images I acquired in the
>> Zeiss LSM format.
>> Since the last ImageJ-update only a small number of images in the *.mdb
>> archive  is accessible by the LOCI-plugin.
>>      
> There was a bug in the 4.1.0 release of Bio-Formats that sounds very
> similar to the problem that you describe; however, this bug was fixed
> in the latest (4.1.1) release.  As it's not clear which version of
> Bio-Formats you are using, could you please make sure that you are
> using the 4.1.1 release?  The version number can be found by selecting
> "Help>  About Plugins>  LOCI Plugins".
>
> If the problem occurs with 4.1.1, then as Johannes mentioned, it would
> be very helpful if you could provide a more complete description of
> the problem.  In particular, it would be helpful if you could send any
> error messages that you see.
>
> Regards,
> -Melissa
>
> On Mon, Feb 15, 2010 at 2:56 AM, Markus Böttcher
> <[hidden email]>  wrote:
>    
>> Hi...
>>
>> I have always used the LOCI-plugin to work with my images I acquired in the
>> Zeiss LSM format.
>> Since the last ImageJ-update only a small number of images in the *.mdb
>> archive  is accessible by the LOCI-plugin.
>> Does anyone know how to solve that problem?
>>
>> thanks and
>> best regards,
>> Markus
>>
>>      
>    

[Melissa Linkert-2]

Hi Markus,

Thank you for sending additional information.  Unfortunately, I cannot
reproduce the problem with the Zeiss LSM datasets that I have.  Would
you be willing to send one of the problematic datasets to aid in
debugging?  You can place data on the LOCI FTP server, details for
which will be sent off-list.

Regards,
-Melissa

On Tue, Feb 16, 2010 at 4:20 AM, Markus Böttcher
<[hidden email]> wrote:

> Hi Melissa,
>
> The latest stable release (built 3rd dec 2009, revision 5727) and ImageJ
> 1.43q are installed on my computer...
> I'm sorry that I can't send any error messages because there are no error
> messages.
> Starting the loci-plugin as:
> plugins -> loci -> databrowser -> selecting the *.mdb file
> results in an overview of only a small number of images that are included in
> the *.mdb archive...
>
> best regards,
> Markus
>
> PS.:
> I'm new to the mailing list and would like to say that I'm glad that there
> are lot people trying to help each other... thanks a lot...
>
> Am 15.02.2010 21:51, schrieb Melissa Linkert:
>>
>> Hi Markus,
>>
>>
>>>
>>> I have always used the LOCI-plugin to work with my images I acquired in
>>> the
>>> Zeiss LSM format.
>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>> archive  is accessible by the LOCI-plugin.
>>>
>>
>> There was a bug in the 4.1.0 release of Bio-Formats that sounds very
>> similar to the problem that you describe; however, this bug was fixed
>> in the latest (4.1.1) release.  As it's not clear which version of
>> Bio-Formats you are using, could you please make sure that you are
>> using the 4.1.1 release?  The version number can be found by selecting
>> "Help>  About Plugins>  LOCI Plugins".
>>
>> If the problem occurs with 4.1.1, then as Johannes mentioned, it would
>> be very helpful if you could provide a more complete description of
>> the problem.  In particular, it would be helpful if you could send any
>> error messages that you see.
>>
>> Regards,
>> -Melissa
>>
>> On Mon, Feb 15, 2010 at 2:56 AM, Markus Böttcher
>> <[hidden email]>  wrote:
>>
>>>
>>> Hi...
>>>
>>> I have always used the LOCI-plugin to work with my images I acquired in
>>> the
>>> Zeiss LSM format.
>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>> archive  is accessible by the LOCI-plugin.
>>> Does anyone know how to solve that problem?
>>>
>>> thanks and
>>> best regards,
>>> Markus
>>>
>>>
>>
>>
>

[Melissa Linkert-2]

Hi Markus,

Thank you for sending a dataset off-list.  The latest trunk build of
Bio-Formats (available at http://loci.wisc.edu/bio-formats/downloads)
will open all of the images in your dataset.

Regards,
-Melissa

On Wed, Feb 17, 2010 at 10:23 AM, Melissa Linkert
<[hidden email]> wrote:

> Hi Markus,
>
> Thank you for sending additional information.  Unfortunately, I cannot
> reproduce the problem with the Zeiss LSM datasets that I have.  Would
> you be willing to send one of the problematic datasets to aid in
> debugging?  You can place data on the LOCI FTP server, details for
> which will be sent off-list.
>
> Regards,
> -Melissa
>
> On Tue, Feb 16, 2010 at 4:20 AM, Markus Böttcher
> <[hidden email]> wrote:
>> Hi Melissa,
>>
>> The latest stable release (built 3rd dec 2009, revision 5727) and ImageJ
>> 1.43q are installed on my computer...
>> I'm sorry that I can't send any error messages because there are no error
>> messages.
>> Starting the loci-plugin as:
>> plugins -> loci -> databrowser -> selecting the *.mdb file
>> results in an overview of only a small number of images that are included in
>> the *.mdb archive...
>>
>> best regards,
>> Markus
>>
>> PS.:
>> I'm new to the mailing list and would like to say that I'm glad that there
>> are lot people trying to help each other... thanks a lot...
>>
>> Am 15.02.2010 21:51, schrieb Melissa Linkert:
>>>
>>> Hi Markus,
>>>
>>>
>>>>
>>>> I have always used the LOCI-plugin to work with my images I acquired in
>>>> the
>>>> Zeiss LSM format.
>>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>>> archive  is accessible by the LOCI-plugin.
>>>>
>>>
>>> There was a bug in the 4.1.0 release of Bio-Formats that sounds very
>>> similar to the problem that you describe; however, this bug was fixed
>>> in the latest (4.1.1) release.  As it's not clear which version of
>>> Bio-Formats you are using, could you please make sure that you are
>>> using the 4.1.1 release?  The version number can be found by selecting
>>> "Help>  About Plugins>  LOCI Plugins".
>>>
>>> If the problem occurs with 4.1.1, then as Johannes mentioned, it would
>>> be very helpful if you could provide a more complete description of
>>> the problem.  In particular, it would be helpful if you could send any
>>> error messages that you see.
>>>
>>> Regards,
>>> -Melissa
>>>
>>> On Mon, Feb 15, 2010 at 2:56 AM, Markus Böttcher
>>> <[hidden email]>  wrote:
>>>
>>>>
>>>> Hi...
>>>>
>>>> I have always used the LOCI-plugin to work with my images I acquired in
>>>> the
>>>> Zeiss LSM format.
>>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>>> archive  is accessible by the LOCI-plugin.
>>>> Does anyone know how to solve that problem?
>>>>
>>>> thanks and
>>>> best regards,
>>>> Markus
>>>>
>>>>
>>>
>>>
>>
>

[Markus Böttcher]

Hi Melissa...

thanks a lot for resolving the problem promptly :-)...

best regards,
Markus

Am 18.02.2010 19:27, schrieb Melissa Linkert:

> Hi Markus,
>
> Thank you for sending a dataset off-list.  The latest trunk build of
> Bio-Formats (available at http://loci.wisc.edu/bio-formats/downloads)
> will open all of the images in your dataset.
>
> Regards,
> -Melissa
>
> On Wed, Feb 17, 2010 at 10:23 AM, Melissa Linkert
> <[hidden email]>  wrote:
>    
>> Hi Markus,
>>
>> Thank you for sending additional information.  Unfortunately, I cannot
>> reproduce the problem with the Zeiss LSM datasets that I have.  Would
>> you be willing to send one of the problematic datasets to aid in
>> debugging?  You can place data on the LOCI FTP server, details for
>> which will be sent off-list.
>>
>> Regards,
>> -Melissa
>>
>> On Tue, Feb 16, 2010 at 4:20 AM, Markus Böttcher
>> <[hidden email]>  wrote:
>>      
>>> Hi Melissa,
>>>
>>> The latest stable release (built 3rd dec 2009, revision 5727) and ImageJ
>>> 1.43q are installed on my computer...
>>> I'm sorry that I can't send any error messages because there are no error
>>> messages.
>>> Starting the loci-plugin as:
>>> plugins ->  loci ->  databrowser ->  selecting the *.mdb file
>>> results in an overview of only a small number of images that are included in
>>> the *.mdb archive...
>>>
>>> best regards,
>>> Markus
>>>
>>> PS.:
>>> I'm new to the mailing list and would like to say that I'm glad that there
>>> are lot people trying to help each other... thanks a lot...
>>>
>>> Am 15.02.2010 21:51, schrieb Melissa Linkert:
>>>        
>>>> Hi Markus,
>>>>
>>>>
>>>>          
>>>>> I have always used the LOCI-plugin to work with my images I acquired in
>>>>> the
>>>>> Zeiss LSM format.
>>>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>>>> archive  is accessible by the LOCI-plugin.
>>>>>
>>>>>            
>>>> There was a bug in the 4.1.0 release of Bio-Formats that sounds very
>>>> similar to the problem that you describe; however, this bug was fixed
>>>> in the latest (4.1.1) release.  As it's not clear which version of
>>>> Bio-Formats you are using, could you please make sure that you are
>>>> using the 4.1.1 release?  The version number can be found by selecting
>>>> "Help>    About Plugins>    LOCI Plugins".
>>>>
>>>> If the problem occurs with 4.1.1, then as Johannes mentioned, it would
>>>> be very helpful if you could provide a more complete description of
>>>> the problem.  In particular, it would be helpful if you could send any
>>>> error messages that you see.
>>>>
>>>> Regards,
>>>> -Melissa
>>>>
>>>> On Mon, Feb 15, 2010 at 2:56 AM, Markus Böttcher
>>>> <[hidden email]>    wrote:
>>>>
>>>>          
>>>>> Hi...
>>>>>
>>>>> I have always used the LOCI-plugin to work with my images I acquired in
>>>>> the
>>>>> Zeiss LSM format.
>>>>> Since the last ImageJ-update only a small number of images in the *.mdb
>>>>> archive  is accessible by the LOCI-plugin.
>>>>> Does anyone know how to solve that problem?
>>>>>
>>>>> thanks and
>>>>> best regards,
>>>>> Markus
>>>>>
>>>>>
>>>>>            
>>>>
>>>>          
>>>        
>>      
>