Mutliview Deconvolution PSF Format

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Mutliview Deconvolution PSF Format

nellypledge
Hi all,
Can anybody please advise on the correct format for the PSF that can be provided to the multiview reconstruction deconvolution plugin by Stephan Preibisch.
Also, how does the pixel size of that PSF change things?  Both if I let it find them from the reference beads and if I provide a PSF (assumed) zstack.

Thanks
Neil

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Re: Mutliview Deconvolution PSF Format

Stephan Preibisch
Hi Anthony,

it should be 3d Tiff with the same calibration as the input data. It will apply the same transformation to the PSF(s) as to each respective stack that us deconvoled.

Hope this helps,
Stephan

Sent from my iPhone

> On May 5, 2016, at 23:36, Pavel Tomancak <[hidden email]> wrote:
>
>
> Begin forwarded message:
>
>> From: "Anthony, Neil" <[hidden email]>
>> Subject: Mutliview Deconvolution PSF Format
>> Date: May 5, 2016 7:53:45 PM GMT+02:00
>> To: [hidden email]
>> Reply-To: [hidden email]
>>
>> Hi all,
>> Can anybody please advise on the correct format for the PSF that can be provided to the multiview reconstruction deconvolution plugin by Stephan Preibisch.
>> Also, how does the pixel size of that PSF change things?  Both if I let it find them from the reference beads and if I provide a PSF (assumed) zstack.
>>
>> Thanks
>> Neil
>>
>> ________________________________
>>
>> This e-mail message (including any attachments) is for the sole use of
>> the intended recipient(s) and may contain confidential and privileged
>> information. If the reader of this message is not the intended
>> recipient, you are hereby notified that any dissemination, distribution
>> or copying of this message (including any attachments) is strictly
>> prohibited.
>>
>> If you have received this message in error, please contact
>> the sender by reply e-mail message and destroy all copies of the
>> original message (including attachments).
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Mutliview Deconvolution PSF Format

nellypledge
In reply to this post by nellypledge
Thanks Stephan.

Am I correct in saying it's a a stack from a single view?

Also, can you advise on the pixel dimensions (e.g. 7x7x11 vs 15x15x9) both for user calibrated and auto generated?

Thanks
Neil

________________________________
From: [hidden email]
Sent: May 6, 2016 2:37 AM
To: Anthony, Neil
Cc: [hidden email]
Subject: Fwd: Mutliview Deconvolution PSF Format

Hi Anthony,

it should be 3d Tiff with the same calibration as the input data. It will apply the same transformation to the PSF(s) as to each respective stack that us deconvoled.

Hope this helps,
Stephan

Sent from my iPhone

Begin forwarded message:

From: Pavel Tomancak <[hidden email]<mailto:[hidden email]>>
Date: May 5, 2016 at 23:36:09 GMT+2
To: "[hidden email]<mailto:[hidden email]> Preibisch" <[hidden email]<mailto:[hidden email]>>
Subject: Fwd: Mutliview Deconvolution PSF Format


Begin forwarded message:

From: "Anthony, Neil" <[hidden email]<mailto:[hidden email]>>
Subject: Mutliview Deconvolution PSF Format
Date: May 5, 2016 7:53:45 PM GMT+02:00
To: [hidden email]<mailto:[hidden email]>
Reply-To: [hidden email]<mailto:[hidden email]>

Hi all,
Can anybody please advise on the correct format for the PSF that can be provided to the multiview reconstruction deconvolution plugin by Stephan Preibisch.
Also, how does the pixel size of that PSF change things?  Both if I let it find them from the reference beads and if I provide a PSF (assumed) zstack.

Thanks
Neil

________________________________

This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.

If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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Re: Mutliview Deconvolution PSF Format

Stephan Preibisch
Hi,

yes, it is one single stack per view or one single stack for all views.

The size of the stack depends on the size of your PSF, i.e. Magnification, Lightsheet diameter etc. You have to look at your images and see how big it has to be in order to cover the entire PSF. I am sorry that I cannot be more precise here. But usually it is bigger than the sizes you suggested.

Cheers,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute of Medical Systems Biology of the MDC
Building 89, 1.08b

email: [hidden email] <mailto:[hidden email]>
web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>

> On 06 May 2016, at 23:44, Anthony, Neil <[hidden email]> wrote:
>
> Thanks Stephan.
>
> Am I correct in saying it's a a stack from a single view?
>
> Also, can you advise on the pixel dimensions (e.g. 7x7x11 vs 15x15x9) both for user calibrated and auto generated?
>
> Thanks
> Neil
>
> From: [hidden email]
> Sent: May 6, 2016 2:37 AM
> To: Anthony, Neil
> Cc: [hidden email]
> Subject: Fwd: Mutliview Deconvolution PSF Format
>
> Hi Anthony,
>
> it should be 3d Tiff with the same calibration as the input data. It will apply the same transformation to the PSF(s) as to each respective stack that us deconvoled.
>
> Hope this helps,
> Stephan
>
> Sent from my iPhone
>
> Begin forwarded message:
>
>> From: Pavel Tomancak <[hidden email] <mailto:[hidden email]>>
>> Date: May 5, 2016 at 23:36:09 GMT+2
>> To: "[hidden email] <mailto:[hidden email]> Preibisch" <[hidden email] <mailto:[hidden email]>>
>> Subject: Fwd: Mutliview Deconvolution PSF Format
>>
>>
>> Begin forwarded message:
>>
>>> From: "Anthony, Neil" <[hidden email] <mailto:[hidden email]>>
>>> Subject: Mutliview Deconvolution PSF Format
>>> Date: May 5, 2016 7:53:45 PM GMT+02:00
>>> To: [hidden email] <mailto:[hidden email]>
>>> Reply-To: [hidden email] <mailto:[hidden email]>
>>>
>>> Hi all,
>>> Can anybody please advise on the correct format for the PSF that can be provided to the multiview reconstruction deconvolution plugin by Stephan Preibisch.
>>> Also, how does the pixel size of that PSF change things?  Both if I let it find them from the reference beads and if I provide a PSF (assumed) zstack.
>>>
>>> Thanks
>>> Neil
>>>
>>> ________________________________
>>>
>>> This e-mail message (including any attachments) is for the sole use of
>>> the intended recipient(s) and may contain confidential and privileged
>>> information. If the reader of this message is not the intended
>>> recipient, you are hereby notified that any dissemination, distribution
>>> or copying of this message (including any attachments) is strictly
>>> prohibited.
>>>
>>> If you have received this message in error, please contact
>>> the sender by reply e-mail message and destroy all copies of the
>>> original message (including attachments).
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>
>>
>


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Re: Mutliview Deconvolution PSF Format

nellypledge
Thanks Stephan, I appreciate the details.

I have ORCA cameras with a relatively small area.  I've opted for undersampling in favor of more area so my PSF will likely be smaller.

Thanks
Neil