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+ Measuring Time-Lapse Experiments: An Overview
+ Kota Miura (Centre for Molecular and Cellular Imaging, EMBL),
+.June.2006
+{ EMBO Practical Course 2006}
+{ “Microinjection and Detection of Probes” }
+**Abstract**
+Time series of digital images, usually called ‘a stack’, contains
+temporal dynamics of position and intensity. By analyzing these
+dynamics, we can extract numerical parameter which then enables us to
+characterize the biological system. There are three types of dynamics.
+(i) Position does not change but intensity changes over time. (ii)
+Position changes but the intensity does not change. (iii) Both Position
+and Intensity change over time. Since (iii) is a combination of (i) and
+(ii), I will explain the basics of the measurement of type (i) and (ii).
+An example of type (i) is the measurement of cargo transport dynamics in
+vesicle trafficking (Hirschberg et al., 1998). Transition of protein
+localization from ER to Golgi then to the plasma membrane was measured
+over time by measuring the signal intensity in each statically
+positioned compartment. This type of technique has evolved to various
+sophisticated methods based on the same principle such as FRAP
+technique. Type (ii) corresponds to the measurement of movement, or
+object tracking, and an example is the single particle tracking of
+membrane surface proteins (Murase et al., 2004).
+{ Notes}
+{ Single Particle Tracking (SPT)}
+(Saxton and Jacobson, 1997)  A review on SPT, also discusses about
+mean-square-displacement plot and interpretations.
+(Kusumi et al., 1993)  Excellent application of SPT on constrained
+diffusion.
+(Qian et al., 1991) Theoretical Comparison of SPT and FRAP
+(Miura, 2005) A review on tracking techniques in cell biology.
+Active Contour (SNAKES) Demo
+<http://www.markschulze.net/snakes/>
+{ FRAP reviews}
+Reviews on FRAP (Phair et al., 2004; Sprague and McNally, 2005). Another
+review is a bit older, but good for overviewing classic literatures
+(Reits and Neefjes, 2001)[^1].
+{ Models for FRAP analysis}
+**Diffusion:** Axelrod *et. al.*’s paper is a frequently cited classic
+paper on FRAP (Axelrod et al., 1976). They measured pure diffusion.
+Closed solution for Axelrod’s model was proposed later and still used by
+many researchers (Soumpasis, 1983).
+Several empirical formula for fitting diffusion-FRAP can be found in
+other literatures (Ellenberg et al., 1997; Yguerabide et al., 1982).
+**Reaction:** Jacquez ‘s book is good for learning the compartmental
+analysis used for modelling reaction-dominant FRAP recovery  (Jacquez,
+) The book is also informative and excellent for modelling
+biochemical dynamics in general. Recent advances in biochemistry
+incorporate interaction with immobile (non-diffusive) entity, which
+radically changes the interpretation of parameter acquired by fitting
+exponential equations (Bulinski et al., 2001; Sprague et al., 2004)
+{ Advanced Models for FRAP}
+**Diffusion-Reaction:** Formula considering both diffusion and reaction
+were recently proposed (Sprague et al., 2004). This paper is interesting
+not only for this diffusion-reaction approach but also for derivation of
+pure-diffusion, effective diffusion and reaction dominant FRAP.
+**Considerations on Membrane Architecture:** Mobility of proteins is
+generally constrained by the complex architecture of intracellular
+space, the shape of organelle. Such steric effects has been omitted from
+FRAP analysis for the estimation mobility parameters e.g. diffusion
+coefficient.  Recent literature includes this effect for the FRAP
+analysis by reconstructing the ER membrane geometry by 3D rendering and
+simulating the movement of protein along that geometry (Sbalzarini et
+al., 2006; Sbalzarini et al., 2005).
+{ Cytoplasmic Architecture}
+Diffusion within cytoplasm is not a simple pure-diffusion.
+Cytoskeletons, organelle and supramolecular complexes become obstacles
+to the movement of proteins. In a very small scale, the vacant spaces
+between these structures allow the molecule to move around without
+encountering these structures. In this vacant space, the cytoplasmic
+viscosity is said to be similar to water, or 2-3 folds higher than
+water. Measurement of small scale diffusion needs special techniques. On
+the other hand, we also can measure the movement of molecules in a
+larger scale. In this case, diffusion encounters steric hindrances and
+bindng/reaction with other molecules. Diffusion coefficient that
+includes this slowing factor is thus an *apparent diffusion*. More
+specifically when the molecule mobility is slowed down due to
+binding/reactions, this type pf diffusion is called *effective
+diffusion*.
+To know more about microscopic diffusion and macroscopic diffusion
+inside cell, refer to Luby-Phelps papers (Luby-Phelps, 1994;
+Luby-Phelps, 2000).
+{ ImageJ website}
+Free and powerful software for quantitative image analysis.
+http://rsb.info.nih.gov/ij/
+{ EAMNET (European Advanced Microscopy Network) website}
+http://www.embl.de/eamnet/
+The website is maintained by Stefan Terjung (ALMF, EMBL). Download page
+links to many useful Macros for analyzing image-stacks.
+{ References}
+[^1]:  Good for overviewing FRAP; but I don’t agree with statement such
+    as below; Quote:  “*When motion due to active transport or
+    unidirectional flow can be discounted, protein mobility in a cell is
+    due to brownian motion.*”, because mobility in this case is defined
+    by Brownian motion *and *the structural environment, which makes the
+    FRAP curve fitting difficult.
+</markdown>