[OpenSPIM] SCAPE

[Balki K]

Hi Johannes,

I am thinking in the direction Johannes suggested - adapt OpenSPIM to
include SCAPE.

I still have a question:

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

In the article (Page 6 - SCAPE image analyisis and visualization) the
authors say that

"Three-dimensional volume renderings were generated using volren modules in
Amira
using custom colourmaps. All data shown are in SCAPE (x′–y′–z′) image space
(Fig. 1b).

The SCAPE data shown in Fig. 2e, Supplementary Fig. 7 and Supplementary
Movie 2
were corrected for the skewing effect of the oblique light sheet by
shifting each depth
plane laterally by a constant, linear factor....... ".

I am not familiar with Amira (and Volren modules in that). But, is it so
straightforward as stated
OR
involves a rigorous geometrical and computational work?

If the authors of the article are seeing this, please help us understand!

Best regards,
Balki



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
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