/Transgenic-songbird-neuron-migration

Primary LanguageMATLAB

GitHub Repository (Transgenic-songbird-neuron-migration) for the following publication:

In Vivo Imaging in Transgenic Songbirds Reveals Superdiffusive Neuron Migration in the Adult Brain (2024) Naomi R. Shvedov, Sina Analoui, Theresia Dafalias, Timothy J. Gardner, Benjamin B. Scott

  1. /Transgenic-songbird-neuron-migration/Fig4-TrackVisualization/

    • Code to plot the spatial positions and relative displacement of cell tracks in 3D, color-coded by time.

  2. /Transgenic-songbird-neuron-migration/Fig5-CollectiveMigration/

    • Data and code to analyze and plot pairwise correlations in speed and heading direction of all cells from multiple birds (CollectiveMigrationFigureCorrelations.m).
    • Also includes a script to analyze and plot the entropy in position and headings across the population of one bird (CollectiveMigrationFigureEntropy.m).

  3. /Transgenic-songbird-neuron-migration/Fig6-SuperdiffusiveMigration/

    • All necessary code to recreate Figure 6. Compute_MSDfunction.m is called in PopulationSuperdiffusivityPlots.m script, which fits the diffusion model.

  4. /Transgenic-songbird-neuron-migration/Fig7-Simulation/

    • This generative model is meant to simulate the migration of newborn neurons in HVC of juvenile songbirds as a stepwise process.
    • No additional file downloads are required, simulation can be downloaded and run as is.
    • Running this file yields a 3D representation of HVC that is intersected by the VZ with the birth and end points of simulated cells plotted in green and red, respectively.
    • Users can define how long the simulation is run, how many cells are being simulated, and if they want to plot the traces of each cell's migration path (See: User-Defined Parameters for Simulation Run)

  5. /Transgenic-songbird-neuron-migration/Functions/

    • All functions that are called in above code.

  6. /Transgenic-songbird-neuron-migration/ProcessedData/

    • Contains all data from experiments, both compiled (combined_ALL) and separated for each bird (/IndividualBirdData/).
    • Data was tracked manually from registered and denoised 3D+t in vivo time-lapses taken with a two-photon microscope for >3 hours.
    • Data was pre-processed to remove cells with tracks that are too short, or are mis-clicks by the manual tracker.
    • Cells that have a tortuosity above 7 or a displacement below 5 were filtered out, as those were most likely tracked stationary cells.
    • dynamic_stats.mat files contain information for every cell position at every timepoint, including individual step distances and the real times of observation.
    • neuroblast_stats.mat files have the statistics for every cell track individually (e.g. total speed, tortuosity, total displacement, etc.).

The data columns are labeled with abbreviations. The key is as follows:

FOR DYNAMIC STATS

  • N --> neuron ID
  • I --> Intensity (a.u.)
  • X,Y,Z --> Location in X,Y,Z respectively, in microns
  • Slice --> the specific depth in the imaging Z-stack
  • F --> the "frame" or timepoint of observation
  • T --> extracted timestamp from metadata
  • Q --> data was split up into 4 quadrants for easier tracking
  • R --> region. 1 = HVC. 0 = hyperpallium/nidopallium
  • S --> session. number of sessions varies across birds.
  • MaxX,Y,Z,F --> X,Y,Z,F dimensions of whole quadrant
  • Bird_ID --> shorthand bird identifier
  • Age --> age of bird
  • Sex --> 1 = male, 0 = female
  • fixedQ --> 1 = quadrants were restitched after separation, XYZ positions are accurate relative to each other for all cells
  • H --> How many hours have elapsed since first timepoint of that cell
  • pathdiffs, pathXdiffs,pathYdiffs,pathZdiffs --> step size (Euclidean 3D distance between current and last position and X,Y,Z components, respectively)
  • XY/XZangles --> step-wise heading direction in radians
  • delt_XY/XZangles --> change in angle between current and previous step
  • thresh... --> same as above except after a step distance threshold of 5 is applied
  • instvel --> instantaneous velocity, path distance over time since last step
  • currentdisp/X/Y/Z --> cumulative displacement from starting position in 3D and in X,Y,Z components

FOR NEUROBLAST STATS

  • pathtot (and pathX/Y/Z) --> total distance traveled by cell, both in 3D and in X/Y/Z components
  • meanZpos --> average depth of cell
  • duration --> length of observation in hours
  • ...
  • (see above)
  • ...
  • disptot (and dispX/Y/Z) --> total displacement of cell relative to start, both in 3D and in X/Y/Z components
  • torts --> cell tortuosity
  • speed --> total distance/total time
  • dispXY/XZangle --> overall heading of displacement vector
  • std/avg_threshdeltXY/XZ* --> average or St. Dev of thresholded (see above) changes in angle of all steps of cell
    • If cell travels in a straight line and does not deviate, the average thresh. deltXY/XZ will be 0, and St. Dev would be small

doi: 10.5281/zenodo.10476669