davidbreuer / img2net

Automated network-based analysis of imaged phenotypes

img2net

Automated network-based analysis of imaged phenotypes

(A) GUI to set parameters for the network reconstruction. (B) Actin network reconstructed with a hexagonal grid. (C) 3D reconstruction for image data with four z-slices. (D) Time series of the assortativity for multiple untreated (blue) and treated (red) plants. (E) Ratios of average path lengths and algebraic connectivities of observed and null model networks.

Please see project website for details.

Instructions

Install package via:

• sudo pip2 install -e .

Run program via:

• run_img2net.py OR
• cd bin && python2 run_img2net.py

Citation

If this software is useful for your work, please include the following references in your publication or redistribution:

Breuer et al. (2014) Quantitative analyses of the plant cytoskeleton reveal underlying organizational principles. J. R. Soc. Interface, 11(97): 20140362.

Breuer and Nikoloski (2014) img2net: Automated network-based analysis of imaged phenotypes. Bioinformatics, 30(22): 3291-3292.

img2net's Issues

AttributeError: class img2net has no attribute 'calc'

Traceback (most recent call last):
  File "run_img2net.py", line 70, in on_button1_clicked
    img2net.calc.calc(self,gtk,dir_input,gridtype,nullmodel,R,lz,dx,dy,dz,pbx,pby,pbz,vax,vay,cores)
AttributeError: class img2net has no attribute 'calc'

As I list img2net's methods/attributes, the result below:

>>> dir(img2net)
['__builtins__', '__doc__', '__file__', '__name__', '__package__', '__path__', '__version__']