Re: Newbie Needs Ada Advice

[ezkcdude <zamir.evan@gmail.com>]

On May 8, 4:21 pm, Markus E Leypold
<development-2006-8ecbb5cc8aREMOVET...@ANDTHATm-e-leypold.de> wrote:
> ezkcdude <zamir.e...@gmail.com> writes:
> > All helpful responses. Thanks. One idea that now makes some sense
> > (having thought about it for all of a couple of hours), is that the
> > GUI/interface could be a separate application that simply sets up the
> > experiment (i.e. microscope configuration). For example, creating an
> > XML document with appropriate hardware parameters, and then feeding
> > this document to the "engine", which actually controls the microscope.
>
> Don't use XML for that. Overkill. Just plain old tagged data lines
>
>    param1  2342.2423
>    param2  32423.234
>
> or even a 1-line per call
>
>    CALL function_name 1212 123123 123 1112
>
> will suffice and be more readable. Imap uses lispish lists as interface.
>
> Regards -- Markus

Well, maybe if I explain the experiment better, it will make more
sense, why I can't do this so simply. Basically, we do time-lapse
imaging of several (living) specimens (usually quail embryos, but
could also be cell culture) over the course of a few hours to days.
For each specimen, there are several illumination modes (brightfield +
1 or more fluorescence channels). On top of  that the microscope stage
is moved to several overlapping "tiles" for each specimen, so a
widefield montage can be later stitched together in post-processing.
Finally, we capture several slices in the z-direction, which can be
collapsed according to a focus score (sort of like an auto-focus
routine). Again, that can be done in post-processing. Anyway, to
illustrate, here is a typical example:

Experiment:
6 embryos
2x4 tiles
7 z-planes
3 illumination modes
12 minutes/frame (5 frames/h)

Each grayscale image that is acquired is about 635K, so for one 12-
hour experiment, we're acquiring 6*8*7*3*5*12*635K~38GB!

And I need to mention that the embryos do not simply stay put, they
can move around enough that periodic adjustments to the microscope
must be made. That is why it is so important to have some graphical
feedback. I must be able to make sure the embyro is positioned
correctly, and this will obviously vary from embryo-to-embryo and
between experiments. Well, if that still sounds easy to you...