In snjy9182/smt-beta: Statistical analysis of single molecule trajectories

knitr::opts_chunk$set(echo = TRUE)

Data Generation

All the single molecule imaging data was generated using wide-field epi-illumination microscope. Single molecules were tracked using DiaTrack v3.05 software. Single molecule images were collected after pre-bleach of initial intense fluorescence (glow), and 405-nm laser excitation was added as needed to maintain desired fluorophore detection density (reference to a manuscript will be added soon which contains detailed information on imaging regime setup).

Folders of Imaging Data

--- HSF and HSF_2

Single molecule tracking data of Heat Shot Factor (HSF) in Drosophila, HSF is labeled with Halo tag. Data is a courtesy of Xiaona Tang.

--- HTZ1 and ImageJ

Single molecule tracking data of histone variant HTZ1 in fission yeast, HTZ1 is labeled with Halo tag. Data is a courtesy of Anand Ranjan.

--- SWR1 and SWR1_2

Single molecule tracking data of histone variant HTZ1 chromatin remodelers SWR1 in fission yeast, SWR1 is labeled with Halo tag. Data is a courtesy of Anand Ranjan.

Within each folder,

_MASK.tif, are mask files for removing background, generated by thresholding images from initial fluorescence (glow).
_Nuclei.tif, are the Nuclei images for plotting, generated by the DIC image of the cell.
.mat files are the matlab file outputs from tracking software Diatrack;
.csv files are the matlab file outputs from Diatrack converted to .csv by first reading the .mat files with createTrackll() and exporting to .csv files with exportTrackll(). The .csv files from exportTrackll() have the same format as output files from ImageJ plugin Particle Tracker. There are also no functional difference between the tracklls created from .mat or .csv files; however, .csv files are used here for their small file sizes and faster reading.

Other Folders

--- INDEX

componentTrackID-SWR1.comp.1.csv
componentTrackID-SWR1.comp.1.csv

Index files which contains indices of trajectories that are of different component, generated by selComponentTracks() when output set to be TRUE. It used for plotting trajectories of different component.