The code that relates to work described in Khetan et al. (2021) and a current manuscript in preparation. The code takes in data points and a boundary and outputs tesselations with packing distributions (histograms of polygon frequency).
REFERENCE:
- Khetan N, Pruliere G, Hebras C, Chenevert J and Athale CA. (2021) Self-organized optimal packing of kinesin-5-driven microtubule asters scales with cell size. J Cell Sci. 134(10):jcs257543. DOI:10.1242/jcs.257543
- Khetan N, Athale CA. (2022), Tessellation based quantitative framework for the spatial analysis of subcellular structures. Biophys. J. 121, 521a. DOI:10.1016/j.bpj.2021.11.2741
Following are the step-wise instructions to execute the program.
Version and Libraries dependencies Please install the following:
- Python version 3.7.7
- Numpy
- Scipy
- shapely
- pylab
- matplotlib
Usuage for master branch Execute the following in the shell command line
python AsterQuant_V6.py
Output files generated in the following folders:
<output_fig>
This contains:
1. display_Voronoi >> Data points and Voronoi tessellated image
2. Overlays_Voronoi >> Overlays above with the raw image if required
3. RawVoronoi >> Voronoi image alone
4. VorStats >> composite figure ; with plots of histogram of polygonality, NND, area , length distributions and measures such as circularity , eutacticty
5. VorStatsCorrelation >> continued from #4,
<output_files>
Main file-names
1. AllEutactest.out >> euctactic measure
2. All_NND.out >> near neighbor distance (NND) for each Voronoi cell
3. polygonAreaLength.out >> polygonality, area and lengths of/from each polygons
4. measures.csv >> stores all the regularity measures
Scripts
1. AsterQuant_V6.py
2. compute_functions.py
3. coordinate_merger.py
4. plot_Quantvoronoi.py
5. plot_voronoi.py
6. AsterQuant_V6_B.py.ipynb
Folder structure
- expt // These contain input files and images
- sim // These contain input files and images
- output_fig and // to store the outputs from a run - IMAGES
- output_files // to store the outputs from a run - MEASURES and ANALYSED DATA ( Representative output files and images from phallusia, nematodes and simulations included )
- Make sure "output_fig" and "output_files " exists in the directory
- Usage: USer needs to provide the following inputs - Line # 75 -90 along with the description. filenameImage , px2micron , extn , outfilename, u_scale, method , selectImage , FnameAsterCoor
Forked from @ https://github.com/khetanneha/AsterQuant
The work pursued 2017- 2021 shared in 3 branches as explained below:
-
Branch (master) :post-jcs-2021. Updates on the many different measures for analysis and from different systems, post JCS paper in 2021.
-
Branch: v3_jcs. Parts of the work published in Khetan N, Pruliere G, Hebras C, Chenevert J and Athale CA. (2021) Self-organized optimal packing of kinesin- 5-driven microtubule asters scales with cell size. J Cell Sci. 134(10):jcs257543
-
Branch: AsterQuant. Development until 2021, JCS
Please refer to the file: README_AsterQuant.md in this depository for further details.