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attempt to clarify and improve the current article on PhotoActivated Localization Microscopy, restructuring the text and images, providing links to other wikipedia articles and connecting it to the super-resolution page of wikipedia.

# Photo Activated Localization Microscopy and Stochastic Optical Reconstruction Microscopy

## Introduction

Photo Activated Localization Microscopy (PALM or fPALM) [1] [2] and Stochastic Optical Reconstruction Microscopy (STORM) [3] are widefield (as opposed to point scanning techniques such as laser scanning confocal microscopy) fluorescence microscopy imaging methods that allow obtaining images with a resolution beyond the diffraction limit. The methods were proposed in 2006 in the wake of a general emergence of optical super resolution microscopy methods, and were featured as Methods of the Year for 2008 by the Nature Methods Journal [4]. The development of PALM as a targeted biophysical imaging method was largely prompted by the discovery of new species and the engineering of mutants of fluorescent proteins displaying a controllable photochromism, such as Photo Activatable GFP. However it should be noted that the concomitant development of STORM, sharing the same fundamental principle, made originally use of paired cyanine dyes. One molecule of the pair (called activator), when excited near its absorption maximum, serves to reactivate the other molecule (called reporter) to the fluorescent state.

A growing number of dyes are used for PALM, STORM and related techniques, both organic fluorophores and fluorescent proteins. Some are compatible with live cell imaging, other allow faster acquisition or the denser labeling. The choice of a particular fluorophore ultimately depends on the application and on its underlying photophysical properties [5].

Both techniques have undergone significant technical developments[6], in particular allowing multicolor imaging and the extension to three dimensions, with the current axial resolution limit of 10 nm obtained using an interferometric approach with two opposing objectives collecting the fluorescence from the sample[7].

## Concept

Conventional fluorescence microscopy is performed by selectively staining the sample with fluorescent molecules, either lined to antibodies as in immunohistochemistry or using fluorescent proteins fused to the genes of interest. Typically, the more concentrated the fluorophores, the better the contrast of the fluorescence image.

A single fluorophore can be visualized under a microscope (or even under the naked eye [8]) if the number of photons emitted is sufficiently high, and in contrast the background is low enough. The precision that can be achieved to localize an point emitter scales as the inverse square root of the number of emitted photons.

The ability to identify as two individual entities two closely spaced fluorophores is limited by the diffraction of light, and quantified by the Abbe’s criterion that the minimal distance that allows to resolve two point sources is given by

${\displaystyle d={\frac {\lambda }{2NA}}}$

where ${\displaystyle \lambda }$ is the wavelength of the fluorescent emission and NA is the numerical aperture of the microscope. However, if the emission from the two neighboring fluorescent molecules is made distinguishable, i.e. the photons coming from each of the two can be identified, then it is possible to overcome the diffraction limit [9]. Once a set of photons from a specific molecule is collected, its image in the light microscope corresponds to a diffraction limited spot, the Point Spread Function of that microscope. The center of this molecule can be localized with a precision larger than the Point Spread Function (or the Abbe criterion minimal distance) by fitting the observed emission profile to a known geometrical function, typically a Gaussian in two or three dimensions.

Multiple closely spaced emitters are indistinguishable. The position of a point source can be recovered only if the photons it emitted have been identified from those arising from the neighboring molecules

The two steps of identification and localization of individual fluorescent molecules in a dense environment where many are present are at the basis of PALM, STORM and their development.

Although many approaches to molecular identification exist, the light induced photochromism of selected fluorophores developed as the most promising approach to distinguish neighboring fluorophores by separating their fluorescent emission in time. By turning on stochastically sparse subsets of fluorophores with light of a specific wavelength, individual molecules can be then excited and imaged according to their spectra. To avoid the accumulation of active fluorophores in the sample, that would eventually bring back to a diffraction limited image, the spontaneously occurring phenomenon of photobleaching is exploited in PALM, whereas reversible switching between a fluorescent on-state and a dark off-state of a dye is exploited in STORM.

Photoactivation, Localization and Bleaching

In summary, PALM and STORM are based on collecting under a fluorescent microscope a large number of images each containing just a few active isolated fluorophores. The imaging sequence allows for the many emission cycles according to stochastic activation of fluorescence from non-emissive (or less emissive) state to a bright state, and back to a non-emissive or bleached state. During each cycle, the density of activated molecules is kept low enough that the images of individual fluorophores do not typically overlap.

Single CCD frame displaying individual fluorescent proteins excited in Total Internal Reflection
Sequence of frames containing single molecule images

### Localization of individual fluorophores

In each image of the sequence the position of a fluorophore is calculated with a precision typically greater than the diffraction limit, in the typical range of a few to 20 nm, and the resulting information of the position of the centers of all the localized molecules represent the super-resolution PALM or STORM image.

The localization precision ${\displaystyle \sigma }$ can be calculated according to the formula: ${\displaystyle \sigma ={\sqrt {\left({\frac {s_{i}^{2}+{\frac {a^{2}}{12}}}{N}}\right)\cdot \left({\frac {16}{9}}+{\frac {8\pi s_{i}^{2}b^{2}}{a^{2}N}}\right)}}}$ where N is the number of collected photon, a is the pixel size of the imaging detector, b^2 is the average background signal and s_i is the standard deviation of the Point Spread Function. [10] The requirement of localizing at the same time multiple fluorophores simultaneously over an extended area determines the reason why these methods are wide-field, employing as a detector a CCD or a CMOS camera.

The requirement of an enhanced signal to noise ratio to maximize localization precision determines the frequent combination of this concept with widefield fluorescent microscopes allowing optical sectioning, such as Total Internal Reflection Microscopes or Light Sheet Microscopy.

## The Super Resolution Image

The resolution of the final image is limited by the precision of each localization and the number of localizations instead of diffraction. The super resolution image is therefore a pointillistic representation of the coordinates of all the localized molecules. The super-resolution image is commonly rendered by representing each molecule in the image plane as a two dimensional Gaussian with amplitude proportional to the number of photons collected, and the standard deviation depending on the localization precision.

Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy. Scale bar in (A–E) indicates 1 µm. Scale bar in (F–H) indicates 50 nm. [11]

## Technical Developments

### Multicolor PALM/STORM

Strategies for multicolor localization microscopy. Left: spectral separation. Center: multiple activators (STORM). Right: Ratiometric imaging

The peculiar photophysical properties of the fluorophores employed in PALM/STORM super resolution imaging pose both constraints and opportunities for multicolor imaging. Three strategies have emerged so far: excitation of spectrally separated fluorophores using an emission beamsplitter [12], using of multiple activators/reporters in STORM mode [13][14] and ratiometric imaging of spectrally close fluorophores [15].

### Three Dimensional Imaging

Although originally developed as 2D (x, y) imaging methods, PALM and STORM have quickly developed into 3D (x,y, z) capable techniques. To determine the axial position of a single fluorophore in the sample the following approaches are currently being used: modification of the Point Spread Function to introduce z-dependent features in the 2D (x,y) image (the most common approach is to introduce astigmatism in the PSF); multiplane detection, where the axial position is determined by comparing two images of the same PSF defocused one with respect to the other; interferometric determination of the axial position of the emitter using two opposed objectives and multiple detectors [7]; use of temporal focusing to confine the excitation/activation; use of light sheet excitation/activation to confine to a few hundred nanometers thick layer arbitrarily positioned along the z-plane within the sample.

### Live Cell Imaging

The requirement for multiple cycles of activation, excitation and de-activation/bleaching would typically imply extended periods of time to form a PALM/STORM image, and therefore to operate on a fixed sample, a number of works have been published as early as 2007 [16] performing PALM/STORM on live cells. The ability to perform live super-resolution imaging using these techniques ultimately depends on the technical limitations of collecting enough photons from a single emitter in a very short time. This depends both on the photophysical limitations of the probe as well as on the sensitivity of the detector employed. Relatively slow (seconds to tens of seconds) processes such as modification in the organization of focal adhesions have been investigated be means of PALM [17], whereas STORM has allowed to image faster processes such as membrane diffusion of clathrin coated pits or mitochondrial fission/fusion processes. A promising application of live cell PALM is the use of photoactivation to perform high density single particle tracking (sptPALM [18]), overcoming the traditional limitation of single particle tracking to very diluted systems.

## Differences between PALM and STORM

PALM and STORM share a common fundamental principle, and the numerous developments tend to make the two techniques even more intertwined. Still they differ in several technical details and a fundamental point. On the technical side, PALM was performed on a biological specimen using endogenously expressed fluorophores, in the form of genetic fusion constructs to a photoactivatable fluorescent protein. STORM used instead immunolabeling of the sample with antibodies tagged with organic fluorophores. In both cases the fluorophores are driven by light between an active-ON and an inactive-OFF state. In PALM, however, photoactivation and photobleaching confine the life of the fluorophore to a limited interval of time, and a continuous emission of the fluorophore is desirable in between without any fluorescence intermittency. In STORM stochastic photoblinking of the organic fluorophores (typically brighter than fluorescent proteins) was originally exploited to separate neighboring dyes. In this respect, the more robust the blinking, the higher the probability of distinguishing two neighbouring fluorophores.

In this respect, several research works have explored the potential of PALM to perform a quantitation of the number of fluorophores (and therefore proteins of interest) present in a sample by counting the activated fluorophores [11] [19][20].

The approach used to treat the fluorescent dynamics of the fluorescent label used in the experiments will determine the final appearance of the super-resolution image, and the possibility to determine an unambiguous correspondence between a localization event and a protein in the sample.

## References

1. ^ E. Betzig, G. H. Patterson, R. Sougrat, O. W. Lindwasser, S. Olenych, J. S. Bonifacino, M. W. Davidson, J. Lippincott-Schwartz, H. F. Hess (2006). "Imaging Intracellular Fluorescent Proteins at Nanometer Resolution". Science. 313 (5793): 1642–1645.
2. ^ S. T. Hess, T. P. Giriajan, M. D. Mason (2006). "Ultra-high resolution imaging by Fluorescence Photoactivation Localization Microscopy". Biophysical Journal. 91 (11): 4258–4272.
3. ^ M. J. Rust, M. Bates, X. Zhuang (2006). "Sub diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)". Nature Methods. 3 (20): 793–796.
4. ^ "Method of the Year 2008". Nature Methods. 6 (1): 1–109. 2009.
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8. ^ W. E. Moerner, D. P. Fromm (2003). "Methods of single-molecule fluorescence spectroscopy and individual fluorescence probes". Review of Scientific Instruments. 74 (8): 3597–3619.
9. ^ E. Betzig (1995). "Proposed Method for molecular optical imaging". Optics Letters. 20 (3): 237–239.
10. ^ K. I. Mortensen, L S. Churchman, J. A. Spudich and H. Flyvbjerg (2010). "Optimized localization analysis for single-molecule tracking and super-resolution microscopy". Nature Methods. 7 (5): 377–381.
11. ^ a b Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS; et al. (2009). "Self-Organization of the Escherichia coli Chemotaxis Network Imaged with Super-Resolution Light Microscopy.". PLoS Biology. 7 (6). doi:10.1371/journal.pbio.1000137.
12. ^ Shroff H, Galbraith CG, Galbraith JA, White H, Gillette J, Olenych S, Davidson MW, Betzig E (2007). "Dual-color superresolution imaging of genetically expressed probes within individual adhesion complexes". Proceedings of the National Academy of Sciences. 104 (51): 20308–20313.
13. ^ M Bates, B Huang, GT Dempsey, X Zhuang (2007). "Multicolor Super Resolution Imaging with Photo-Switchable fluorescent probes". Science. 317 (5845): 1749–1753.
14. ^ Bock, H. (2007). "Two-color far-field fluorescence nanoscopy based on photoswitchable emitters". Applied Physics B. 88 (2): 161–165. Bibcode:2007ApPhB..88..161B. doi:10.1007/s00340-007-2729-0. Unknown parameter |coauthors= ignored (|author= suggested) (help)
15. ^ Testa I, Wurm CA, Medda R, Rothermel E, von Middendorf C, Folling J, Jakobs S, Schonle A, Hell SW, Eggeling C. (2010). "Multicolor fluorescence nanoscopy in fixed and living cells by exciting conventional fluorophores with a single wavelength". Biophysical Journal. 99: 2686–2694.
16. ^ Hess, Samuel T. and Gould, Travis J. and Gudheti, Manasa V. and Maas, Sarah A. and Mills, Kevin D. and Zimmerberg, Joshua, (2007). "Dynamic clustered distribution of hemagglutinin resolved at 40 nm in living cell membranes discriminates between raft theories,". Proceedings of the National Academy of Sciences. 104 (44): 17370–17375.
17. ^ Shroff, H., C. G. Galbraith, J. A. Galbraith, and E. Betzig (2008). "Live-cell photoactivated localization microscopy of nanoscale adhesion dynamics". Nature Methods. 5 (44): 417–423.
18. ^ S Manley, J M Gillette, G H Patterson, H Shroff, H F Hess, E Betzig & J Lippincott-Schwartz (2008). "High-density mapping of single-molecule trajectories with photoactivated localization microscopy". Nature Methods. 5: 155 – 157.
19. ^ P Annibale, S Vanni, M Scarselli, U Rothlisberger, A Radenovic (2011). "Quantitative Photo Activated Localization Microscopy:Unraveling the Effects of Photoblinking". PLoS One. 6: p.e22678, 07.
20. ^ Lee, Sang-Hyuk and Shin, Jae Yen and Lee, Antony and Bustamante, Carlos (2012). "Counting single photoactivatable fluorescent molecules by photoactivated localization microscopy (PALM)". Proceedings of the National Academy of Sciences. 109 (43): 17436–17441.