Addition of frames

[Martin Ward]

Hi,

I have a series of stills that I would like to be able to add together  
to form a pseudo-long exposure image.  The footage in question is from  
a series of laser scattering experiments.  If possible, the plugin  
would provide an accumulated image of particles that pass through the  
beam over time and can avoid build up of background noise  
(accumulation of the background noise from the probe laser beam).  I  
assume the required pre-processing could be preformed in image J  
currently, however I have not managed to find a plugin that can add  
together the frames as I require.

If anyone on the mailing list known of a source, or a person I could  
contact about this I would be very grateful if you could let me know.

Regards,
Martin.

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[Adrian Daerr-2]

Hello Martin,

It is not clear to me how you distinguish noise from signal on your
images. Can you explain what is wrong with simply adding all images
together ? Your signal should increase linearly with the number of
images, whereas the noise will increase only with the square root.
You just have to use an accumulator whose pixel values will not overflow
or produce rounding errors, such as 16bit for the accumulation of up to
257 8bit-images, or better 32bit float, which will work without
precautions for (at least) up to 65536 8bit-images. If you have longer
runs to add up, you must either accumulate into a double-type array (not
a native ImageJ1 image type, but safe for up to 2^45 images) or properly
group your additions.

hope this helps,
Adrian



On 09.07.2013 11:57, Martin Ward wrote:

> Hi,
>
> I have a series of stills that I would like to be able to add together
> to form a pseudo-long exposure image.  The footage in question is from a
> series of laser scattering experiments.  If possible, the plugin would
> provide an accumulated image of particles that pass through the beam
> over time and can avoid build up of background noise (accumulation of
> the background noise from the probe laser beam).  I assume the required
> pre-processing could be preformed in image J currently, however I have
> not managed to find a plugin that can add together the frames as I require.
>
> If anyone on the mailing list known of a source, or a person I could
> contact about this I would be very grateful if you could let me know.
>
> Regards,
> Martin.
>

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[Adrian Daerr-2]

[I hope you don't mind me putting the ImageJ list back into the
recipient list; as long as nothing confidential is being disclosed, a
discussion that started publicly should IMHO remain public, others might
be interested in the subject]

Hi Martin,

> Yes, perhaps I should have made myself clearer.  During the laser
> scattering experiments, we see rare objects passing through the probe
> beam.  The rest of the time, we see a background haze from the probe
> laser passing through the solution.

I see. In that case I'd try to find a criterion that identifies images
with an object (e.g. there are more than so-and-so-many pixels with a
brightness above X; there is a round blob with such-and-such
characteristics; ...), and average only over those. Of course care has
to be taken so as not to bias the observable, but if you include some
images in a time interval around the events of interest, this should not
be much of a problem.

happy research,
Adrian

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[Michael Schmid]

Hi Martin,

what you could also try is not adding the slices but rather take the maximum intensity in Image>Stacks>Z Project.

To convert your single images into a stack, either use Image>Stacks>Images to Stack or open all the files as an Image Sequence (assuming that they are all in the same directory); then you get a stack immediately and you can also do preprocessing on the whole stack.

Without knowing what kind of noise you have, it is impossible to suggest a method for preprocessing.

Michael
________________________________________________________________

2013-07-09 11:57, Martin Ward wrote:
> Hi,
>
> I have a series of stills that I would like to be able to add together to form a pseudo-long exposure image.  The footage in question is from a series of laser scattering experiments.  If possible, the plugin would provide an accumulated image of particles that pass through the beam over time and can avoid build up of background noise (accumulation of the background noise from the probe laser beam).  I assume the required pre-processing could be preformed in image J currently, however I have not managed to find a plugin that can add together the frames as I require.
>
> If anyone on the mailing list known of a source, or a person I could contact about this I would be very grateful if you could let me know.
>
> Regards,
> Martin.

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