Time-averaged simulation results and in vivo measurements to show the impact of red blood cells on the flow field in the cortical microvasculature

2018-07-19T05:10:58Z (GMT) by Franca Schmid

The dataset contains in 5 files. 4 of them are time-averaged results of blood flow simulations with discrete red blood cell (RBC) tracking in realistic microvascular networks. The 5th file contains median values of RBC velocity measurements at capillary bifurcations in the somatosensory cortex of the mouse.

Further notes on the simulation results:
- The realistic microvascular networks are from the mouse parietal cortex and have first been published in Blinder et al., 2013, Nature Neuroscience (https://doi.org/10.1038/nn.3426).
- The numerical model to simulate blood flow in realistic microvascular networks has been described in Schmid et al., 2017, PLOS Computational Biology (https://doi.org/10.1371/journal.pcbi.1005392).
- MVN1 and MVN2 stands for microvascular network 1 and 2, respectively.
- wRBCs and wpPs stands for 'with red blood cells' and 'with passive particles'. These terms describe two different numerical models. Further information will be added upon publication of the underlying manuscript.

NOTE: Further information on the precise simulation setup and the in vivo RBC velocity measurements will be available as soon as the manuscript has been accepted for publication.

File format: pickle (Python)

Files 1 - 4 (Time-averaged simulation results):
Filenames: MVN1_wpPs.tar.bz2, MVN2_wpPs.tar.bz2, MVN1_wRBCs.tar.bz2, MVN2_wRBCs.tar.bz2

Each compressed folder contains two files:

edgesDict.pkl: dictionary with edge/vessel related data: 

  • flow: Flow rate in vessel [µm^3/ms]
  • length: Vessel length [µm] (Tortuosity is considered)
  • htt: Tube hematocrit in vessel [-]
  • diameter: Effective vessel diameter [µm]
  • connectivity: Vertex indices, e.g. start and end vertex of the corresponding vessel

verticesDict.pkl: dictionary with vertex/bifurcation related data:

  • index: Index of the current vertex 
  • coords: Coordinates to describe the position of the vertex [µm]
  • pressure: Pressure at the vertex [mmHg]


File 5 (in vivo RBC velocity measurements):
Filename: measurementDict.pkl


  • divergent_d1: divergent bifurcation, RBC velocity measurement in daughter vessel 1
  • divergent_d2: divergent bifurcation, RBC velocity measurement in daughter vessel 2
  • convergent_m1: convergent bifurcation, RBC velocity measurement in mother vessel 1
  • convergent_m2: convergent bifurcation, RBC velocity measurement in mother vessel 2

Data structure: list of list,
e.g. daughter vessel 1:
[[bif.1 - measure.1, bif.1 - measure.2, bif.1 - measure.3], [bif.2 - measure.1, bif.2 - measure.2, bif.2 - measure.3],...]
bif.: bifurcation, measure.: measurement.
The order of bifurcations is the same for 'divergent_d1' and 'divergent_d2' (and for 'convergent_m1' and 'convergent_m2').