Request: Define a per-localization Z uncertainty

[GoogleCodeExporter]

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 lechrist...@gmail.com on 28 Apr 2014 at 5:28

[GoogleCodeExporter]

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 comment by krize...@gmail.com on 2 May 2014 at 9:43

[GoogleCodeExporter]

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-continue
s-about-localization-and-super-resolution-td7581644.html

Cheers

Cheers,

Christophe

Original comment by lechrist...@gmail.com on 2 May 2014 at 9:57

[GoogleCodeExporter]

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 comment by zitmen@gmail.com on 6 May 2014 at 10:19

• Changed state: Accepted
• Added labels: Type-Enhancement
• Removed labels: Type-Defect