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# Soans_et_al_opticalcup_surface
## About
This repository contains the scripts and documentation associated to the publication:
Script for publication - Matrix topology guides collective cell migration in vivo
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**Matrix topology guides collective cell migration in vivo**
Karen Grace Soans, Ana Patricia Ramos, Jaydeep Sidhaye, Abhijeet Krishna, Anastasia Solomatina, Karl Hoffmann, Raimund Schlüßler, Jochen Guck, Ivo. F Sbalzarini, Carl Modes, Caren Norden
## Script
**`extractDerotatedSurface_v1.0_threshHuang.py`**
Goal: Extract a projection of a tilted surface. This Fiji script extracts a projection of a tilted surface of derotated selected regions of the image (optical cup) to align the surface as much as possible with the xy plane. The surface is then extracted (height map + reslicing) and max-projected.
## Usage & Disclaimer
The scripts are provided as is, without the intention that an interested reader will be able to run them directly. The authors share their scripts here, not a ready-to-use tool. Still, they should provide enough technical detail to allow replicating the analyses.
## License
The scripts are provided as is under [BSD3 License](https://opensource.org/licenses/BSD-3-Clause).
## Support
For further support please contact [Norden Lab](https://gulbenkian.pt/ciencia/research-groups/cnorden/) (mail: cnorden@igc.gulbenkian.pt) or Scientific Computing Facility (mail: scicomp@mpi-cbg.de).
## DOI
This repository is resolvable via: https://dx.doi.org/adddoihere with the [GWDG](https://www.gwdg.de/en/application-services/persistent-identifier-pid/epic-pid-search) assigned PID: XXX
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