[OpenSPIM] SCAPE and SPIM

[Johannes Schindelin]

Hi Balki,

On 2015-01-20 05:57, Balki K wrote:

> I am a new entrant into SPIM as well this forum.

Welcome! ;-)

> I have been asked to explore building a mSPIM system for our institute. 
> But
> yesterday there was an update on a new type of system called SCAPE.
> 
> Please have a look at the online version of the publication in Nature
> Photonics from Hillman's group in Columbia University, NY.

We are all busy, so it is a good practice to include a link if you 
already have one handy. I looked it up and I *think* you refer to this 
one?

http://www.nature.com/nphoton/journal/vaop/ncurrent/full/nphoton.2014.323.html

Unfortunately, I am not at a computer which can access the full text 
(and even more unfortunate: the authors did not upload preprints to 
arxiv nor bioRxiv) and you will understand that $32 is a bit much just 
to be able to analyze the technique for you ;-)

> I have a clear understanding of SPIM system. But SCAPE is new to me. Is
> there someone who is familiar with the two different systems that can
> explain the pros & cons o SCAPE system?

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.

With those caveats in mind, my interpretation is that their microscope 
uses a scanning mirror (or cantilever) to move the light sheet through 
the specimen, and that the light sheet is not perpendicular to the 
acquisition axis but at an oblique angle.

The OpenSPIM setup we published uses a stage to move the specimen 
instead of the light sheet (which means that the optical sections are 
parallel, unlike the sections obtained by rotating the light sheet with 
a cantilever – even if they are *almost* parallel in practice). Further, 
in the OpenSPIM setup, the images have uniform pixel spacings because 
the light sheet is perpendicular to the acquisition axis, while the 
pixel spacings in images acquired by the SCAPE microscope differ not 
only depending on the current angle of the light sheet but also on the 
exact coordinate on the image plane.

The major difference, therefore, appears that the SCAPE microscope can 
be much faster (because it moves the light sheet much faster), at the 
expense of requiring a sophisticated reconstruction algorithm because of 
the non-uniform pixel spacings (read: point spread functions).

It would be really cool if you could adapt the OpenSPIM setup to support 
SCAPE microscopy; You should make sure that you have access to a gifted 
mathematician with intermediate programming skills to implement the 
image reconstruction (read: the all-too-common half-hearted Matlab 
snippet won't do at all).

Looking forward to your progress!
Johannes