Request: Define a per-localization Z uncertainty

[zitmen]

Hi,

Congratulations for the paper. I'd like to request an enhancement:

Would it be possible for ThunderSTORM to include a column for z uncertainty, and to
treat x, y, and z uncertainty the same way (i.e. possibility to have a fixed value
for all localizations, or a defined value for each localizations?)

I am using ThunderSTORM merely for displaying localizations calculated by another software,
and I'd like to calculate the Z uncertainty for each localization event before displaying
it.

Thanks a lot,

Christophe

Original issue reported on code.google.com by lechristophe on 2014-04-28 17:28:46

[zitmen]

A new column for z uncertainty and visualization by itself shouldn't be a problem. But
can you give us a hint how to calculate it? It is not so easy because you need to combine
errors originating from averaging several calibration curves obtained by focusing through
a sample with beads and errors originating from the detected number of photons.

Original issue reported on code.google.com by krizekp1 on 2014-05-02 09:43:27

[zitmen]

You are right that calculating the Z uncertainty is difficult!

For a start, I'd like to make the Z uncertainty proportional to the XY uncertainty:
Uz = coef*Uxy with coef around 2. As both depends primarily on the photon count, it
would be more rigorous than using a fixed Z uncertainty (although it's still quick
and dirty). Specifying coef=1 (Uz = Uxy) would also allow me to replicate the reconstruction
generated by the Nikon N-STORM software if needed (although it is unrealistic... I've
asked them about that).

When I get more time, I'll try to get a rigorous expression for Uz using the calibration
curve fit and this reference:

Rieger B, Stallinga S. The lateral and axial localization uncertainty in
super-resolution light microscopy. 
Chemphyschem. 2014 Mar 17;15(4):664-70.
doi:10.1002/cphc.201300711. 
http://onlinelibrary.wiley.com/doi/10.1002/cphc.201300711/abstract

Not sure how difficult it will be... I think someone from your lab (Zdenek Svindrych)
has helped me when I discussed this on the Confocal List: 
http://confocal-microscopy-list.588098.n2.nabble.com/discussion-is-open-continues-about-localization-and-super-resolution-td7581644.html

Cheers

Cheers,

Christophe

Original issue reported on code.google.com by lechristophe on 2014-05-02 09:57:07

[zitmen]

Hi, the feature of fetching the Z uncertainty has been added in commit 30e07de007ea
and is now available in the latest daily build. The uncertainty isn't calculated automatically
yet. However if you supply a data with column called "uncertainty_z [nm]" then the
rendering module will take it into account. You can easily add the column in your favorite
spreadsheet processor.

The automatic calculation of Z uncertainty will be implemented later. Thanks for the
literature. We will put together a formula that fits our algorithm best. Until then
we will keep this issue open so you are informed when the formula is implemented.

Original issue reported on code.google.com by zitmen on 2014-05-06 22:19:36

• Labels added: Type-Enhancement
• Labels removed: Type-Defect

[zitmen]

This feature has been implemented in couple of commits between 15th and 18th May 2015 and is now available since daily build dev-2015-05-17-b1.