Back

Interactive 3D visualization and post-processing analysis of vertex-based unstructured polyhedral meshes with ParaView

Sanematsu, P. C.

2021-10-16 biophysics
10.1101/2021.10.15.464601 bioRxiv
Show abstract

The development of physics-based 3D models that investigate the behavior of biological tissues requires effective and efficient visualization tools. The open-source software ParaView has such capabilities, but often impose a steep learning curve due to the use of the Visualization Toolkit (VTK) data structures. To overcome this, I show how to setup the components of 3D vertex-like models, i.e., vertices, faces, and polyhedra, into the VTK data format and then output as ParaView unstructured grid files. I present a few relevant tools to visualize and analyze the files in ParaView. All sample codes are available in the Github repository vis3Dvertex.

Matching journals

The top 8 journals account for 50% of the predicted probability mass.

1
PLOS ONE
5266 papers in training set
Top 12%
15.5%
2
PLOS Computational Biology
1863 papers in training set
Top 3%
10.0%
3
Bioinformatics
1204 papers in training set
Top 4%
5.7%
4
SoftwareX
15 papers in training set
Top 0.1%
5.6%
5
The European Physical Journal E
14 papers in training set
Top 0.1%
4.6%
6
BMC Bioinformatics
457 papers in training set
Top 2%
4.4%
7
Frontiers in Neuroinformatics
41 papers in training set
Top 0.2%
3.3%
8
eLife
5828 papers in training set
Top 38%
2.7%
50% of probability mass above
9
Acta Crystallographica Section D Structural Biology
59 papers in training set
Top 0.2%
2.0%
10
Journal of Open Source Software
25 papers in training set
Top 0.2%
1.8%
11
Scientific Reports
3612 papers in training set
Top 52%
1.8%
12
Journal of Visualized Experiments
34 papers in training set
Top 0.3%
1.8%
13
iScience
1154 papers in training set
Top 16%
1.7%
14
Biophysical Journal
631 papers in training set
Top 3%
1.5%
15
PeerJ
308 papers in training set
Top 6%
1.5%
16
Wellcome Open Research
67 papers in training set
Top 1.0%
1.2%
17
Journal of Chemical Information and Modeling
238 papers in training set
Top 2%
1.1%
18
Biology Open
156 papers in training set
Top 3%
1.0%
19
Frontiers in Physiology
106 papers in training set
Top 3%
0.9%
20
Royal Society Open Science
214 papers in training set
Top 6%
0.9%
21
Viruses
332 papers in training set
Top 4%
0.9%
22
Bioinformatics Advances
203 papers in training set
Top 4%
0.9%
23
Journal of Applied Crystallography
14 papers in training set
Top 0.1%
0.9%
24
European Biophysics Journal
12 papers in training set
Top 0.1%
0.9%
25
eneuro
439 papers in training set
Top 8%
0.6%
26
Computer Methods in Biomechanics and Biomedical Engineering
10 papers in training set
Top 0.3%
0.6%
27
Journal of Computational Chemistry
13 papers in training set
Top 0.3%
0.6%
28
Open Research Europe
14 papers in training set
Top 0.1%
0.6%
29
Gigabyte
62 papers in training set
Top 1%
0.6%
30
Methods
34 papers in training set
Top 0.8%
0.6%