[OpenSPIM] Some early images

[Luke Stuyvenberg]

Hi Pavel & Johannes (and everyone),

On 06/14/13, Pavel Tomancak wrote:
> Nice work. What are the thick, bright, white lines in the image?


The thick lines are flares from tremendously overbright beads.We used 20um beads for this sample, as we were having trouble getting a clean solution of .2um beads. Too much light from the 20um beads gave our Orca's detector a hard time.


On 06/14/13, Johannes Schindelin wrote:
> That is some nice contrast! How many slices did you max-project?


It varies between the images, I believe between 100 and 200 slices.

> Also, as I told Julie on her way out: we absolutely have to use
> off-frequency beads. Our signal is too delicate to be overlaid by beads
> having a field day.


I agree. Before we finished imaging, Julie decided to work with the red beads on Monday; next Thursday we should be able to put together some samples with weaker beads.
 
> This might need some changes on the Wiki to make it *very clear* that you
> should *never* use beads that are excited by exactly the wavelength of the
> laser.


I should point out that these are 20um beads causing the flares. It's possible that sub-resolution beads (even those specifically excited by our laser) won't have the same dramatic effect as these. In other words '*never*' might be a bit overzealous; I'm sure there are times when operators would like a very strong bead signal.

> The page people will read first (if they read any documentation at all,
> that is), is certainly http://openspim.org/Operation (and it does not
> mention the wavelength issue at all). There *is* a section hidden in
> http://openspim.org/Drosophila_embryo_sample_preparation about that, but
> it is unlikely that this page is what people read *before* they image
> their samples and see super-bright beads triggering the full-moon effect.


I agree, of course. It's naive to hope people would read our suggestions for sample prep; I imagine they have a protocol they're already familiar with.
 
> It would be nice, for example, if maybe people from Dresden could
> expand that section, move it to its own page, document there which
> particular beads worked for them (to give a good idea what beads might
> work for others, too), and then link to that page from all the appropriate
> places.

We can probably add a note to the sample prep section on the Operation page, with a link to a page about which beads we've found work well.

Thanks,
Luke