Code and data for Sittewelle & Royle manuscript #p063p036
Passive diffusion accounts for the majority of intracellular nanovesicle transport
Méghane Sittewelle & Stephen J. Royle
Life Sci Alliance 2023. DOI: hhttps://doi.org/10.26508/lsa.202302406
R code for plot recreation.
For details, see the README in plots/
- Several R scripts require TrackMateR to run. Stable release is here, development version is here.
- Some R scripts require TrackMate XML files to process data and generate plots. These files are available at Zenodo together with some of the visualizations generated using TrackMateR.
For FLIP simulation, DiffusionSim.ipf is written for IGOR Pro.
A GUI is available to guide simulations. Click for details...
- Most variables are self-explanatory, please note the units.
- FLIP mode selects between a circle (used in the paper), square or a ring.
- Random start location when checked will start vesicles at random locations throughout the cell. When unchecked, vesicles will start at the cell centre.
- Specify bleach location for circle, square and ring. FlipRingR stipulates the radius of the ring (intended to be used without Random start location checked) so that vesicles diffuse away from the origin before entering the ring. For square specify the left-top (LT) and right-bottom (RB) XY locations relative to the cell centre
(0,0). For circle, an offset can be specified as well as a radius. - Simulate will show the movement of vesicles without FLIP
- FLIP will do a single FLIP simulation
- FLIP Rep will do repeated FLIP simulations
- Visualise if checked will show the tracks when FLIP Rep is clicked.
The bottom part of the panel allows the simulations to be automated by taking a variable number of steps from a start and stop point for FLIP circle radius and for the diffusion coefficient (as described in the paper. Click Automate to start after setting all parameters.
Particle movies were generated using Particle_Simulation.ijm in FIJI.
TrackMate automation is via the groovy script TrackMateAutomation.groovy.
The ground truth outputs can be evaluated in IGOR using VesicleTracks.ipf.
Select Macros > Vesicle Tracks Only or Macros > Vesicle Tracks Simple and select the csv file of the ground truth data that you would like to evaluate.
The "simple" workflow skips algorithmic comparison of tracks and other features which are not necessary for evaluating the ground truth data.
Although not documented in the paper, `VesicleTracks.ipf` will also display movies and tracking data in a neat widget for visualization. Click for details...
To use this, select Macros > Vesicle Tracks... As an input it requires a csv file of tracks and an image.
This is compatible with the outputs from Particle_Simulation.ijm but the display will show all particles in the volume.
The default view shows all particles. Click "show selected" to see the top most directed tracks according to the program.
The TrackMate XML outputs can be analyzed using TrackMateR.
R code to evaluate TrackMate XML files from these routines is available in plots/SJR194/.
Some IGOR procedure files require PXPUtils.ipf to run properly, available here.