*library_books*

## Similar protocols

## Protocol publication

[…] Similarly to the kICS analysis, the SPT analysis was performed separately for each color channel using the **Particle** Tracker plug-in in **ImageJ** as has been described previously . This analysis generates a text file containing the positions of the detected QD particle positions in each image frame as well as linked trajectories describing the motion of individual QDs in time. In this analysis, a major limitation to the use of QDs in SPT is apparent by the generation of a large number of short trajectories rather than a more desirable few very long continuous particle trajectories. In order to minimize the number of inaccurate particle linking events, this analysis was done with very conservative particle linking criteria, corresponding to a particle link range of 5 image frames and a maximum allowed particle displacement of one pixel per image frame. The detected particle motion data was post-processed using custom written Mathematica routines. This post-processing included further linking of particle trajectories by a coincidence search routine in time and space of all trajectories, with a minimal length greater than a cut-off value (here n = 10 to 20 frames) with other trajectories that coincided within space, δr (here set to 8 pixels) but not time. We next calculated the mean squared displacements for each single trajectory, m, that contained n>20 displacements, and for all possible time intervals, nτ, (4)where τ is the acquisition time interval and N is the total number of displacements in a trajectory. The average diffusion coefficient, , of all trajectories for a given molecule and label was then determined by calculating the average mean squared displacements

## Pipeline specifications

Software tools | Particle Tracker, ImageJ |
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Applications | Laser scanning microscopy, Microscopic phenotype analysis |

Organisms | Homo sapiens |