Re: colocalization and focus *commercial response*

[Bitplane Support]

Hi Carl,

According to Bitplane's records, there is a permanent license for Imaris 5.5 registered to you.
Although you can't upgrade it or get support without renewing maintenance, I'm pretty sure that version has the necessary components to apply channel shift corrections.
The simplest approach would be via the Image Processing menu if Imaris ("Channel Shift") -- but the shift units are in pixels/voxels, so you would have to resample the dataset first to achieve sub-voxel shift.

If you had the ImarisTrack module (unfortunately looks like you don't), there is also a "Drift Correction" function that could be applied with sub-voxel precision automatically (first would need to swap the time & channel axes, then correct drift, then swap them back again). 

[Daniel James White]

Hi Kevin and Carl,


Begin forwarded message:

>
> Hi Carl,
>
> According to Bitplane's records, there is a permanent license for Imaris
> 5.5 registered to you.
> Although you can't upgrade it or get support without renewing
> maintenance, I'm pretty sure that version has the necessary components
> to apply channel shift corrections.
> The simplest approach would be via the Image Processing menu if Imaris
> ("Channel Shift") -- but the shift units are in pixels/voxels, so you
> would have to resample the dataset first to achieve sub-voxel shift.

if you resample the data to smaller pixels you need to be very sure how that is done,
so that you dont destroy the intensity data in the image.
Intensities need to be kept nice, since that how the coloc methods asses goodness of signal overlap.

Perhaps Kevin can explain the maths behind how imaris resamples an image to smaller pixels.
I dont see a good explanation in the docs... maybe i missed it.

The only safe resample method is a whole pixel binning...
but that making the pixels bigger.
To make them smaller you need to interpolate somehow...
and the way you do that is critical for not destroying the image intensity data.

Kevin?

>
> If you had the ImarisTrack module (unfortunately looks like you don't),
> there is also a "Drift Correction" function that could be applied with
> sub-voxel precision automatically (first would need to swap the time &
> channel axes, then correct drift, then swap them back again).

Again an explanation of how that really does the maths would be really great,
especially since one must have no black boxes.
or else one can not publish honestly.

Where do i find a mathematical explanation of how this sub pixel image shifting is done,
and how can i be sure image intensities are not destroyed do to a bad interpolation method?
Is it in the docs?

cheers

Dan

>
> Best regards,
> -Kevin
>
> Kevin Frischmann
> Head of Technical Support, US & Canada
> Bitplane, Inc.
> tel: [phone], ext. 11
> fax: [phone]
> [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

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