Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
# Robust Defect Identification
## Description
This software package implements the identification of robust topological defects, where 'robust' means that the topological charges of the identified defects remain unaffected by a certain noise level applied to the two-dimensional vector field in which they are identified.
It applies both to polar and nematic fields, whereby the latter are also known as line fields or orientation fields.
The code was developed by Karl B. Hoffmann during his PhD studies under supervision of Prof. Ivo F. Sbalzarini at the Technical University Dresden, the Center for Systems Biology Dresden, and the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden.
## Citation
When using the software, please cite
> Hoffmann, Karl B. and Sbalzarini, Ivo F. "Robustness of topological defects
> in discrete domains", Physical Review E 103 (2021),
> __https://doi.org/10.1103/PhysRevE.103.012602__
> [pdf also available from __https://sbalzarini-lab.org/docs/Hoffmann2021.pdf__]
A MATLAB implementation of the same concepts was used in this paper as well as for
> Hoffmann, Karl B. and Sbalzarini, Ivo F. "A robustness measure for singular
> point and index estimation in discretized orientation and vector fields",
> Proceedings in Applied Mathematics & Mechanics 20 (2020),
> __https://doi.org/10.1002/pamm.202000261__
> [pdf also available from __https://sbalzarini-lab.org/docs/Hoffmann2020.pdf__]
and for
> Hoffmann, Karl B. and Sbalzarini, Ivo F. "Estimation of unordered core
> size using a robustness measure for topological defects in discretized
> orientation and vector fields", Proceedings in Applied Mathematics &
> Mechanics 21 (2021),
> __https://doi.org/10.1002/pamm.202100105__
> [pdf also available from __https://sbalzarini-lab.org/docs/Hoffmann2021a.pdf__]
See also
> Hoffmann, Karl B.: "Robust Identification of Topological Defects in
> Discrete Vector Fields with Applications to Biological Image Data",
> PhD Thesis at Technical University Dresden, Germany (2022)
## Microscopy image data
The included exampleData-ZebrafishOpticalCup.jpg is courtesy of Karen Soans,
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
It is a 2D maximum projection of Zebrafish Danio rerio optic cup at 18 somite
stage with fluorescent labelling of laminin. For more details see
> Soans, Karen G. and Ramos, Ana Patricia and Sidhaye, Jaydeep and Krishna,
Abhijeet and Solomatina, Anastasia and Hoffmann, Karl B. and Schlüßler, Raimund
> and Guck, Jochen and Sbalzarini, Ivo F. and Modes, Carl D. and Norden, Caren.
> "Collective cell migration during optic cup formation features changing
> cell-matrix interactions linked to matrix topology", Current Biology (2022),
> __https://doi.org/10.1016/j.cub.2022.09.034__
## License
This work is licensed under CC-BY 4.0
## Disclaimer
*IN NO EVENT SHALL THE MOSAIC GROUP BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING
OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE MOSAIC GROUP
HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE MOSAIC GROUP SPECIFICALLY
DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED
HEREUNDER IS ON AN "AS IS" BASIS, AND THE MOSAIC GROUP HAS NO OBLIGATIONS TO
PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.*