How to do frame averaging?

[Mikinka]

Hi all,

I am doing live cell imaging and I would like to do frame averaging such as getting average of 30 image frames to improve signal to background noise ratios. I'm new to ImageJ. Any help would be greatly appreciated.

Thanks!
Mikinka

[Gabriel Landini]

On Sunday 04 March 2007, Mikinka wrote:
> I am doing live cell imaging and I would like to do frame averaging such as
> getting average of 30 image frames to improve signal to background noise
> ratios. I'm new to ImageJ. Any help would be greatly appreciated.

Ideally you should this at the camera (some cameras have an integrator) or
done with the software provided with the manufacturer.

If these are non available, then the alternative is:

grab n images,
convert the images to a stack,
do a stack Z projection using "Average".

This will reduce random image noise by a factor of sqrt(n) but may add some
small degree of blurring.

Cheers,
G.

[Tony Collins-4]

There's Nico Stuurman's Running Zprojector plugin:
http://valelab.ucsf.edu/~nico/IJplugins/Running_ZProjector.html
(You can think of it as a Running TProjector also - sometimes ImageJ
assumes the third dimension is Z but it can equally be T, e.g. "Plot
Z-axis profile" is the same as "Plot intensity vs time").

Have a look at Christopher Philip Mauer's Kalman Filter plugin too.
http://rsb.info.nih.gov/ij/plugins/kalman.html

Regards,
Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Mikinka
> Sent: Sunday, March 04, 2007 7:45 AM
> To: [hidden email]
> Subject: How to do frame averaging?
>
> Hi all,
>
> I am doing live cell imaging and I would like to do frame averaging

such
> as
> getting average of 30 image frames to improve signal to background
noise
> ratios. I'm new to ImageJ. Any help would be greatly appreciated.
>
> Thanks!
> Mikinka
>
> --
> View this message in context: http://www.nabble.com/How-to-do-frame-
> averaging--tf3342300.html#a9295533
> Sent from the ImageJ mailing list archive at Nabble.com.

[Knecht, David]

Nico's Micro-manager plugin for ImageJ (http://micro-manager.org)  
will do frame averaging during acquisition if your camera is  
supported.  Dave

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)


On Mar 4, 2007, at 12:12 PM, Tony Collins wrote:

> There's Nico Stuurman's Running Zprojector plugin:
> http://valelab.ucsf.edu/~nico/IJplugins/Running_ZProjector.html
> (You can think of it as a Running TProjector also - sometimes ImageJ
> assumes the third dimension is Z but it can equally be T, e.g. "Plot
> Z-axis profile" is the same as "Plot intensity vs time").
>
> Have a look at Christopher Philip Mauer's Kalman Filter plugin too.
> http://rsb.info.nih.gov/ij/plugins/kalman.html
>
> Regards,
> Tony
>
> Tony J. Collins, Ph.D.
> McMaster Biophotonics Facility
> Dept. Biochemistry and Biomedical Sciences HSC 4H21A
> McMaster University, Hamilton, ON, L8N 3Z5
> [phone] x28812(off.)/x26488(lab)
> [hidden email]     www.macbiophotonics.ca
>
>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Mikinka
>> Sent: Sunday, March 04, 2007 7:45 AM
>> To: [hidden email]
>> Subject: How to do frame averaging?
>>
>> Hi all,
>>
>> I am doing live cell imaging and I would like to do frame averaging
> such
>> as
>> getting average of 30 image frames to improve signal to background
> noise
>> ratios. I'm new to ImageJ. Any help would be greatly appreciated.
>>
>> Thanks!
>> Mikinka
>>
>> --
>> View this message in context: http://www.nabble.com/How-to-do-frame-
>> averaging--tf3342300.html#a9295533
>> Sent from the ImageJ mailing list archive at Nabble.com.

[Gabriel Landini]

On Sunday 04 March 2007 17:12:45 Tony Collins wrote:
> There's Nico Stuurman's Running Zprojector plugin:
> http://valelab.ucsf.edu/~nico/IJplugins/Running_ZProjector.html
> Have a look at Christopher Philip Mauer's Kalman Filter plugin too.
> http://rsb.info.nih.gov/ij/plugins/kalman.html

I think that 'running averages' (what the running Z projector does) and Kalman
filter are to be used for video *sequences* or streams, not for static series
of images of the same field.
Those two techniques give different weights to each frame in the stream, but
if one wants is to reduce the random element between shots that do not change
to increase S/N, just averaging all the fields is more appropriate.

Cheers,

G.

[Tony Collins-4]

I agree. I assumed the reference to live cell imaging means the images
are part of a video sequence. But your right - if this is just 30 images
of the same frame, a simple average would be best.

Cheers,

Tony

Tony J. Collins, Ph.D.
McMaster Biophotonics Facility
Dept. Biochemistry and Biomedical Sciences HSC 4H21A
McMaster University, Hamilton, ON, L8N 3Z5
[phone] x28812(off.)/x26488(lab)
[hidden email]     www.macbiophotonics.ca

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Gabriel Landini
> Sent: Sunday, March 04, 2007 3:08 PM
> To: [hidden email]
> Subject: Re: How to do frame averaging?
>
> On Sunday 04 March 2007 17:12:45 Tony Collins wrote:
> > There's Nico Stuurman's Running Zprojector plugin:
> > http://valelab.ucsf.edu/~nico/IJplugins/Running_ZProjector.html
> > Have a look at Christopher Philip Mauer's Kalman Filter plugin too.
> > http://rsb.info.nih.gov/ij/plugins/kalman.html
>
> I think that 'running averages' (what the running Z projector does)

and
> Kalman
> filter are to be used for video *sequences* or streams, not for static
> series
> of images of the same field.
> Those two techniques give different weights to each frame in the
stream,
> but
> if one wants is to reduce the random element between shots that do not
> change
> to increase S/N, just averaging all the fields is more appropriate.
>
> Cheers,
>
> G.

[Mikinka]

Thank you for the help.

I'd like to talk about more details. I have been looking for methods for live cell imaging and there is a way to improve signal to background noise ratios by doing two-frame averaging.
So I'm thinking to take 2 frames at acquisition and acquiring images every 10sec intervals for 3mins.
The software attached to the camera doesn't seem to have two-frame averaging function, so that doing Stack Z projection using Average in ImageJ will be useful for me.

Cheers,
Mikinka