Ratiometric imaging

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Ratiometric imaging

Konstanz
Hi,
I would like to rise the question about ratiometric imaging (e.g. with fura-2). Is it possible to have a live tracking for several ROI with recording from 2 channels?

This question was already asked long time ago, but I didn't found any answer.
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Re: Ratiometric imaging

Kline, David D.
Hi. I am not sure an answer has been provided, so I am bumping this email in the hopes that somebody answers. If I missed the answer, then my apologies.

My experience with Fura imaging and uM was to acquire in uM, analyze in FIJI and excel.  

-----Original Message-----
From: Konstanz [mailto:[hidden email]]
Sent: Friday, April 7, 2017 9:47 AM
To: [hidden email]
Subject: [micro-manager-general] Ratiometric imaging

Hi,
I would like to rise the question about ratiometric imaging (e.g. with fura-2). Is it possible to have a live tracking for several ROI with recording from 2 channels?

This question was already asked long time ago, but I didn't found any answer.



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Re: Ratiometric imaging

Konstanz
I didn't get any anwser. I was trying to use 'Z profile stack', but it's not very convinient, gives results only for 1 wavelength & sometimes leads program to freeze.
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Re: Ratiometric imaging

Kline, David D.
The MBF Image J collection had some ratiometric plugins that worked well. That's what we used in the past (and currently until we find another option)

https://imagej.net/MBF_Plugin_Collection
http://imagej.net/mbf/intensity_vs_time_ana.htm#Ratiometric

You can grab those plugins for FIJI via the Cookbook: https://imagej.net/Cookbook

They allow analysis of both 340 and 380, and the ratio.



-----Original Message-----
From: Konstanz [mailto:[hidden email]]
Sent: Monday, May 15, 2017 11:18 AM
To: [hidden email]
Subject: Re: [micro-manager-general] Ratiometric imaging

I didn't get any anwser. I was trying to use 'Z profile stack', but it's not very convinient, gives results only for 1 wavelength & sometimes leads program to freeze.



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Re: Ratiometric imaging

Nico Stuurman-2
In reply to this post by Kline, David D.
Hi David,


On 5/12/17 1:43 PM, Kline, David D. wrote:
> Hi. I am not sure an answer has been provided, so I am bumping this email in the hopes that somebody answers. If I missed the answer, then my apologies.
>
> My experience with Fura imaging and uM was to acquire in uM, analyze in FIJI and excel.
>
> -----Original Message-----
>
>
> I would like to rise the question about ratiometric imaging (e.g. with fura-2). Is it possible to have a live tracking for several ROI with recording from 2 channels?

I don't think this would be particularly hard to write (especially in
2.0), but would need a bit of dedicated time.  Our lab does not
(regularly) do ratiometric imaging, so I never invested the time to do
so.  I believe that CAIRN developed a plugin at some point in time (see
https://www.cairn-research.co.uk/products/image-analysis-software/micro-manager/),
but I have never seen the product (just saw that there is something
online: https://www.cairn-research.co.uk/support/software/).  I also
think that others did similar things.

Best,

Nico

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Re: Ratiometric imaging

Kline, David D.
Thanks Nico.

Your response is appreciated.

Looking at the Cairn website, I do see a mention of possibilities...

" We at Cairn are in the process of adding realtime region intensity plotting so that ╬╝Manager can be used for experiements that our customers have typically required commercial software to achieve."


...but I cannot find a plugin.

Is there something that I can do (or the uManager community) to help generate such a plugin?

Thanks,
Dave



-----Original Message-----
From: Nico Stuurman [mailto:[hidden email]]
Sent: Monday, May 15, 2017 4:07 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] Ratiometric imaging

Hi David,


On 5/12/17 1:43 PM, Kline, David D. wrote:
> Hi. I am not sure an answer has been provided, so I am bumping this email in the hopes that somebody answers. If I missed the answer, then my apologies.
>
> My experience with Fura imaging and uM was to acquire in uM, analyze in FIJI and excel.
>
> -----Original Message-----
>
>
> I would like to rise the question about ratiometric imaging (e.g. with fura-2). Is it possible to have a live tracking for several ROI with recording from 2 channels?

I don't think this would be particularly hard to write (especially in 2.0), but would need a bit of dedicated time.  Our lab does not
(regularly) do ratiometric imaging, so I never invested the time to do so.  I believe that CAIRN developed a plugin at some point in time (see https://www.cairn-research.co.uk/products/image-analysis-software/micro-manager/),
but I have never seen the product (just saw that there is something
online: https://www.cairn-research.co.uk/support/software/).  I also think that others did similar things.

Best,

Nico

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Re: Ratiometric imaging

Konstanz
In reply to this post by Nico Stuurman-2
Hi David,

 Thanks for link, I'll have a look. Actually, for ratiometric post-analysis in ImageJ I produced some plugins.

 However, I have no idea how to do the correct online visualization, during experiments from specified ROIs within Micro-Manager (to have it in parallel with 2D recordings).