scholarly journals Drift correction in localization microscopy using entropy minimization

2021 ◽  
Author(s):  
Carlas Smith ◽  
chirlmin joo ◽  
jelmer Cnossen ◽  
Tao Ju Cui
Keyword(s):  
Drift Correction ◽  
Localization Microscopy ◽  
Entropy Minimization

scholarly journals Sample drift correction in 3D fluorescence photoactivation localization microscopy

2011 ◽  
Vol 19 (16) ◽  
pp. 15009 ◽  
Author(s):  
Michael J. Mlodzianoski ◽  
John M. Schreiner ◽  
Steven P. Callahan ◽  
Katarina Smolková ◽  
Andrea Dlasková ◽  
...  
Keyword(s):  
Drift Correction ◽  
Localization Microscopy

scholarly journals Drift correction in localization microscopy using entropy minimization

2021 ◽  
Author(s):  
Jelmer Cnossen ◽  
Tao Ju Cui ◽  
Chirlmin Joo ◽  
Carlas S Smith
Keyword(s):  
Cross Correlation ◽  
Time Constraints ◽  
Fiducial Markers ◽  
Drift Correction ◽  
Localization Microscopy ◽  
Drift Estimation ◽  
Estimation Precision ◽  
2D And 3D ◽  
Dedicated Hardware ◽  
Compute Time

Localization microscopy offers resolutions down to a single nanometer, but currently requires additional dedicated hardware or fiducial markers to reduce resolution loss from drift of the sample. Drift estimation without fiducial markers is typically implemented using redundant cross correlation (RCC). We show that RCC has sub-optimal precision and bias, which leaves room for improvement. Here, we minimize a bound on the entropy of the obtained localizations to efficiently compute a precise drift estimate. Within practical compute-time constraints, simulations show a 5x improvement in drift estimation precision over the widely used RCC algorithm. The algorithm operates directly on fluorophore localizations and is tested on simulated and experimental datasets in 2D and 3D. An open source implementation is provided, implemented in Python and C++, and can utilize a GPU if available.

scholarly journals Improved localization precision via restricting confined biomolecule stochastic motion in single-molecule localization microscopy

Nanophotonics ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Jielei Ni ◽  
Bo Cao ◽  
Gang Niu ◽  
Danni Chen ◽  
Guotao Liang ◽  
...  
Keyword(s):  
Single Molecule ◽  
Direct Evidence ◽  
Diffraction Limit ◽  
Drift Correction ◽  
Stochastic Motion ◽  
Localization Microscopy ◽  
Alexa Fluor ◽  
Biological Studies ◽  
Localization Precision ◽  
Single Molecule Localization Microscopy

Abstract Single-molecule localization microscopy (SMLM) plays an irreplaceable role in biological studies, in which nanometer-sized biomolecules are hardly to be resolved due to diffraction limit unless being stochastically activated and accurately located by SMLM. For biological samples preimmobilized for SMLM, most biomolecules are cross-linked and constrained at their immobilizing sites but still expected to undergo confined stochastic motion in regard to their nanometer sizes. However, few lines of direct evidence have been reported about the detectability and influence of confined biomolecule stochastic motion on localization precision in SMLM. Here, we access the potential stochastic motion for each immobilized single biomolecule by calculating the displacements between any two of its localizations at different frames during sequential imaging of Alexa Fluor-647-conjugated oligonucleotides. For most molecules, localization displacements are remarkably larger at random frame intervals than at shortest intervals even after sample drift correction, increase with interval times and then saturate, showing that biomolecule stochastic motion is detected and confined around the immobilizing sizes in SMLM. Moreover, localization precision is inversely proportional to confined biomolecule stochastic motion, whereas it can be deteriorated or improved by enlarging the biomolecules or adding a post-crosslinking step, respectively. Consistently, post-crosslinking of cell samples sparsely stained for tubulin proteins results in a better localization precision. Overall, this study reveals that confined stochastic motion of immobilized biomolecules worsens localization precision in SMLM, and improved localization precision can be achieved via restricting such a motion.

scholarly journals A Mean Shift Algorithm for Drift Correction in Localization Microscopy

2021 ◽  
Author(s):  
Frank J Fazekas ◽  
Thomas R Shaw ◽  
Sumin Kim ◽  
Ryan A Bogucki ◽  
Sarah L Veatch
Keyword(s):  
Single Molecule ◽  
Mean Shift ◽  
Time Lapse ◽  
Drift Correction ◽  
Localization Microscopy ◽  
Mean Shift Algorithm ◽  
Peak Finding ◽  
Localization Precision ◽  
Time Lapse Imaging ◽  
Single Molecule Localization Microscopy

Single molecule localization microscopy (SMLM) techniques transcend the diffraction limit of visible light by localizing isolated emitters sampled stochastically. This time-lapse imaging necessitates long acquisition times, over which sample drift can become large relative to the localization precision. Here we present a novel, efficient, and robust method for estimating drift using a simple peak-finding algorithm based on mean shifts that is effective for SMLM in 2 or 3 dimensions.

scholarly journals Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm

2014 ◽  
Vol 22 (13) ◽  
pp. 15982 ◽  
Author(s):  
Yina Wang ◽  
Joerg Schnitzbauer ◽  
Zhe Hu ◽  
Xueming Li ◽  
Yifan Cheng ◽  
...  
Keyword(s):  
Cross Correlation ◽  
Drift Correction ◽  
Localization Microscopy ◽  
Correlation Algorithm

scholarly journals A spectral demixing method for high-precision multi-color localization microscopy

2021 ◽  
Author(s):  
Leonid Andronov ◽  
Rachel Genthial ◽  
Didier Hentsch ◽  
Bruno P Klaholz
Keyword(s):  
Single Molecule ◽  
Nuclear Pore ◽  
Drift Correction ◽  
General Applicability ◽  
Localization Microscopy ◽  
Simultaneous Imaging ◽  
Chromatic Aberrations ◽  
Localization Precision ◽  
The Individual ◽  
Single Molecule Localization Microscopy

Single molecule localization microscopy (SMLM) with a dichroic image splitter can provide invaluable multi-color information regarding colocalization of individual molecules, but it often suffers from technical limitations. So far, demixing algorithms give suboptimal results in terms of localization precision and correction of chromatic aberrations. Here we present an image splitter based multi-color SMLM method (splitSMLM) that offers much improved localization precision & drift correction, compensation of chromatic aberrations, and optimized performance of fluorophores in a specific buffer to equalize their reactivation rates for simultaneous imaging. A novel spectral demixing algorithm, SplitViSu, fully preserves localization precision with essentially no data loss and corrects chromatic aberrations at the nanometer scale. Multi-color performance is further improved by using optimized fluorophore and filter combinations. Applied to three-color imaging of the nuclear pore complex (NPC), this method provides a refined positioning of the individual NPC proteins and reveals that Pom121 clusters act as NPC deposition loci, hence illustrating strength and general applicability of the method.

scholarly journals Real-time adaptive drift correction for super-resolution localization microscopy

2015 ◽  
Vol 23 (18) ◽  
pp. 23887 ◽  
Author(s):  
Ginni Grover ◽  
Wyatt Mohrman ◽  
Rafael Piestun
Keyword(s):  
Real Time ◽  
Super Resolution ◽  
Drift Correction ◽  
Localization Microscopy
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