[OpenSPIM] SCAPE

[Johannes Schindelin]

Hi,

On 2015-01-23 10:08, Balki K wrote:

> You were saying that it requires a sophisticated reconstruction 
> algorithm
> because of the non-uniform pixel spacings.


Yes. As you can see from the figure I linked to earlier:

> Please keep in mind that I bring the software engineering expertise to
> the OpenSPIM project in our lab, not the optics expertise (you probably
> have much more knowledge of optics, given that you are tasked to build 
> a
> microscope). And please keep in mind that I form the following
> understanding only from reading the abstract of the article, supported
> only by the figure at
> http://www.nature.com/nphoton/journal/vaop/ncurrent/fig_tab/
> nphoton.2014.323_F1.html.

... you can actually see for yourself how the pixel spacing differs 
between planes (and possibly between the pixels in each plane).

Now, I am not an optical expert, but I assume you are. So you should be 
in a better position to answer the question how the pixel spacings 
(often called "pixel dimensions") differ.

In practice, it might be that the differences are negligible, both 
within and between planes. If that is the case, you do not need that 
"sophisticated algorithm" I referred to. In that case, you would only 
need to compensate for the obliqueness of the planes, i.e. the fact that 
the planes are *not* perpendicular to the axis along which the plane is 
moved. It will require a little bit of coding and you should make sure 
to have some colleague or employee who can do that for you (I would 
probably use the interpolation algorithms of ImgLib2 to reconstruct the 
volume stacks).

As stated above, you should not take my hunches at face value. It is 
really important that you understand the intrinsic properties of the 
acquisition to reconstruct the images in software. I would be interested 
in that analysis, too, so if you would share it with this mailing list, 
that would be really cool.

Ciao,
Johannes