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malaag7

I’m trying to explore data integration options between Micro-manager and virtual microscopy server, Simagis Live.

Can somebody point me to, or perhaps share, actual examples of multidimensional mosaic structures from Micro-manager?

 

I’m interested in both multi-channel and z-stack mosaics examples.

 

If somebody is interested to collaborate and provide test data, I will be happy to share results of my integration efforts.  My idea is to try loading multilayered image mosaics to Simagis Live virtual microscopy server for easy sharing and server-side analysis.

 

Many thanks,

MaLaag


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Re: new posting

Arthur D. Edelstein
Hi MaLaag,

Your project sounds very interesting. I have recently developed a
Surveyor plugin for Micro-Manager (available soon in the next
Micro-Manager release) that acquires 5D Mosaics (T,X,Y,Z,Channel).
These mosaics are currently tiled during acquisition and each
(T,Z,Chan) mosaic component is saved in a separate TIFF. Every
acquisition contains a Metadata.txt file in JSON format.

Please let me know if you this is what you have in mind. I can acquire
an example mosaic and send it to you off-list. If you are able to
create a utility to transfer image data to Simgas Live then I am sure
this would be of interest to other Micro-Manager users.

Best regards,
Arthur



On Thu, Apr 22, 2010 at 11:28 AM, john malag <[hidden email]> wrote:

> I’m trying to explore data integration options between Micro-manager and
> virtual microscopy server, Simagis Live.
>
> Can somebody point me to, or perhaps share, actual examples of
> multidimensional mosaic structures from Micro-manager?
>
>
>
> I’m interested in both multi-channel and z-stack mosaics examples.
>
>
>
> If somebody is interested to collaborate and provide test data, I will be
> happy to share results of my integration efforts.  My idea is to try loading
> multilayered image mosaics to Simagis Live virtual microscopy server for
> easy sharing and server-side analysis.
>
>
>
> Many thanks,
>
> MaLaag
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>

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Re: new posting

Truant, Ray
Arthur, it would be _very_ handy if deconvolution software like Autodeblur could read that meta data.

Dr. Ray Truant Ph.D
Associate Professor
McMaster University
Department of Biochemistry and Biomedical Sciences
Chair, Huntington Society of Canada Scientific Advisory Board
HSC4N54, 1200 Main Street West
Hamilton, Ontario, Canada L8N3Z5
905-525-9140 ex.22450
905-522-9033 Fax
905-515-5526 blackberry
Skype ray.truant
www.RaytruantLab.ca
www.Macbiophotonics.ca

-----Original Message-----
From: Arthur D. Edelstein [mailto:[hidden email]]
Sent: Thursday, April 22, 2010 3:34 PM
To: Micro-Manager General
Subject: Re: [micro-manager-general] new posting

Hi MaLaag,

Your project sounds very interesting. I have recently developed a
Surveyor plugin for Micro-Manager (available soon in the next
Micro-Manager release) that acquires 5D Mosaics (T,X,Y,Z,Channel).
These mosaics are currently tiled during acquisition and each
(T,Z,Chan) mosaic component is saved in a separate TIFF. Every
acquisition contains a Metadata.txt file in JSON format.

Please let me know if you this is what you have in mind. I can acquire
an example mosaic and send it to you off-list. If you are able to
create a utility to transfer image data to Simgas Live then I am sure
this would be of interest to other Micro-Manager users.

Best regards,
Arthur



On Thu, Apr 22, 2010 at 11:28 AM, john malag <[hidden email]> wrote:

> I'm trying to explore data integration options between Micro-manager and
> virtual microscopy server, Simagis Live.
>
> Can somebody point me to, or perhaps share, actual examples of
> multidimensional mosaic structures from Micro-manager?
>
>
>
> I'm interested in both multi-channel and z-stack mosaics examples.
>
>
>
> If somebody is interested to collaborate and provide test data, I will be
> happy to share results of my integration efforts.  My idea is to try loading
> multilayered image mosaics to Simagis Live virtual microscopy server for
> easy sharing and server-side analysis.
>
>
>
> Many thanks,
>
> MaLaag
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>

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Re: new posting

Arthur D. Edelstein
Hi Ray,

You're right. I should clarify that the Metadata.txt file is what is
produced by Micro-Manager for all 5D Acqusitions (not just mosaics).
For a 3rd-party close-source application it might be necessary to
export the Micro-Manager Metadata to a different format.

Has anyone tried any ImageJ plugins with deconvolution? Or other
deconv applications? Which ones do you like?

Best regards,
Arthur



On Thu, Apr 22, 2010 at 2:01 PM, Truant, Ray <[hidden email]> wrote:

> Arthur, it would be _very_ handy if deconvolution software like Autodeblur could read that meta data.
>
> Dr. Ray Truant Ph.D
> Associate Professor
> McMaster University
> Department of Biochemistry and Biomedical Sciences
> Chair, Huntington Society of Canada Scientific Advisory Board
> HSC4N54, 1200 Main Street West
> Hamilton, Ontario, Canada L8N3Z5
> 905-525-9140 ex.22450
> 905-522-9033 Fax
> 905-515-5526 blackberry
> Skype ray.truant
> www.RaytruantLab.ca
> www.Macbiophotonics.ca
>
> -----Original Message-----
> From: Arthur D. Edelstein [mailto:[hidden email]]
> Sent: Thursday, April 22, 2010 3:34 PM
> To: Micro-Manager General
> Subject: Re: [micro-manager-general] new posting
>
> Hi MaLaag,
>
> Your project sounds very interesting. I have recently developed a
> Surveyor plugin for Micro-Manager (available soon in the next
> Micro-Manager release) that acquires 5D Mosaics (T,X,Y,Z,Channel).
> These mosaics are currently tiled during acquisition and each
> (T,Z,Chan) mosaic component is saved in a separate TIFF. Every
> acquisition contains a Metadata.txt file in JSON format.
>
> Please let me know if you this is what you have in mind. I can acquire
> an example mosaic and send it to you off-list. If you are able to
> create a utility to transfer image data to Simgas Live then I am sure
> this would be of interest to other Micro-Manager users.
>
> Best regards,
> Arthur
>
>
>
> On Thu, Apr 22, 2010 at 11:28 AM, john malag <[hidden email]> wrote:
>> I'm trying to explore data integration options between Micro-manager and
>> virtual microscopy server, Simagis Live.
>>
>> Can somebody point me to, or perhaps share, actual examples of
>> multidimensional mosaic structures from Micro-manager?
>>
>>
>>
>> I'm interested in both multi-channel and z-stack mosaics examples.
>>
>>
>>
>> If somebody is interested to collaborate and provide test data, I will be
>> happy to share results of my integration efforts.  My idea is to try loading
>> multilayered image mosaics to Simagis Live virtual microscopy server for
>> easy sharing and server-side analysis.
>>
>>
>>
>> Many thanks,
>>
>> MaLaag
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
> ------------------------------------------------------------------------------
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>

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Re: new posting

Kurt Thorn
I've used Piotr Wendykier's deconvolution plugins with some success:
http://sites.google.com/site/piotrwendykier/software/deconvolution

They appear to work well but they require a lot of RAM.

Kurt

On 4/22/2010 2:33 PM, Arthur D. Edelstein wrote:

> Hi Ray,
>
> You're right. I should clarify that the Metadata.txt file is what is
> produced by Micro-Manager for all 5D Acqusitions (not just mosaics).
> For a 3rd-party close-source application it might be necessary to
> export the Micro-Manager Metadata to a different format.
>
> Has anyone tried any ImageJ plugins with deconvolution? Or other
> deconv applications? Which ones do you like?
>
> Best regards,
> Arthur
>
>
>
> On Thu, Apr 22, 2010 at 2:01 PM, Truant, Ray<[hidden email]>  wrote:
>    
>> Arthur, it would be _very_ handy if deconvolution software like Autodeblur could read that meta data.
>>
>> Dr. Ray Truant Ph.D
>> Associate Professor
>> McMaster University
>> Department of Biochemistry and Biomedical Sciences
>> Chair, Huntington Society of Canada Scientific Advisory Board
>> HSC4N54, 1200 Main Street West
>> Hamilton, Ontario, Canada L8N3Z5
>> 905-525-9140 ex.22450
>> 905-522-9033 Fax
>> 905-515-5526 blackberry
>> Skype ray.truant
>> www.RaytruantLab.ca
>> www.Macbiophotonics.ca
>>
>> -----Original Message-----
>> From: Arthur D. Edelstein [mailto:[hidden email]]
>> Sent: Thursday, April 22, 2010 3:34 PM
>> To: Micro-Manager General
>> Subject: Re: [micro-manager-general] new posting
>>
>> Hi MaLaag,
>>
>> Your project sounds very interesting. I have recently developed a
>> Surveyor plugin for Micro-Manager (available soon in the next
>> Micro-Manager release) that acquires 5D Mosaics (T,X,Y,Z,Channel).
>> These mosaics are currently tiled during acquisition and each
>> (T,Z,Chan) mosaic component is saved in a separate TIFF. Every
>> acquisition contains a Metadata.txt file in JSON format.
>>
>> Please let me know if you this is what you have in mind. I can acquire
>> an example mosaic and send it to you off-list. If you are able to
>> create a utility to transfer image data to Simgas Live then I am sure
>> this would be of interest to other Micro-Manager users.
>>
>> Best regards,
>> Arthur
>>
>>
>>
>> On Thu, Apr 22, 2010 at 11:28 AM, john malag<[hidden email]>  wrote:
>>      
>>> I'm trying to explore data integration options between Micro-manager and
>>> virtual microscopy server, Simagis Live.
>>>
>>> Can somebody point me to, or perhaps share, actual examples of
>>> multidimensional mosaic structures from Micro-manager?
>>>
>>>
>>>
>>> I'm interested in both multi-channel and z-stack mosaics examples.
>>>
>>>
>>>
>>> If somebody is interested to collaborate and provide test data, I will be
>>> happy to share results of my integration efforts.  My idea is to try loading
>>> multilayered image mosaics to Simagis Live virtual microscopy server for
>>> easy sharing and server-side analysis.
>>>
>>>
>>>
>>> Many thanks,
>>>
>>> MaLaag
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>>
>>>        
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>      
> ------------------------------------------------------------------------------
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>    


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