Metadata-Version: 2.1
Name: Qiber3D
Version: 0.7.0
Summary: Automated quantification of fibrous networks
Home-page: https://github.com/theia-dev/Qiber3D
Author: Anna Jaeschke; Hagen Eckert
Author-email: 
License: MIT
Download-URL: https://github.com/theia-dev/Qiber3D/archive/v0.7.0.zip
Project-URL: Binder, https://mybinder.org/v2/gh/theia-dev/Qiber3D_jupyter/main?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Ftheia-dev%252FQiber3D%26urlpath%3Dtree%252FQiber3D%252Fdocs%252Fjupyter%252Findex.ipynb
Project-URL: Documentation, https://qiber3d.readthedocs.io/
Keywords: Skeleton,Network,Fiber,Reconstruction,Neurons,Vessel,Vascular,confocal,microscopy
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: ~=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: nd2reader (==3.3.0)
Requires-Dist: vedo (==2021.0.5)
Requires-Dist: PIMS (==0.5)
Requires-Dist: tifffile (==2021.10.10)
Requires-Dist: networkx (==2.6.3)
Requires-Dist: matplotlib (==3.4.3)
Requires-Dist: blosc (==1.10.6)
Requires-Dist: openpyxl (==3.0.9)
Requires-Dist: vtk (==9.0.3)
Requires-Dist: kimimaro (==3.0.0)
Requires-Dist: scipy (==1.7.1)
Requires-Dist: tqdm (==4.62.3)
Requires-Dist: scikit-image (==0.18.3)
Requires-Dist: numpy (==1.21.2)
Requires-Dist: Pillow (==8.3.2)
Provides-Extra: kimimaro
Requires-Dist: kimimaro ; extra == 'kimimaro'

# Qiber3D <img src='https://github.com/theia-dev/Qiber3D/raw/master/docs/img/synthetic_animation_silver.gif' align="right"/>
Automated quantification of fibrous networks

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## Setup
    pip install Qiber3D
    
You can install the _latest_ version

    pip install -U git+https://github.com/theia-dev/Qiber3D.git#egg=Qiber3D

or the _dev_ version directly from GitHub.
    
    pip install -U git+https://github.com/theia-dev/Qiber3D.git@dev#egg=Qiber3D

    
## Quick usage

An image stack or a preprocessed network can be loaded with ``Network.load()``
To follow this example, you can download the image stack from figshare under [doi:10.6084/m9.figshare.13655606](https://doi.org/10.6084/m9.figshare.13655606) or use the `Example` class.
```python
import logging
from Qiber3D import Network, config
from Qiber3D.helper import Example, change_log_level

config.extract.nd2_channel_name = 'FITC'
change_log_level(logging.DEBUG)

net_ex = Example.nd2()
net = Network.load(net_ex)
print(net)
# Input file: microvascular_network.nd2
#   Number of fibers: 459 (clustered 97)
#   Number of segments: 660
#   Number of branch points: 130
#   Total length: 16056.46
#   Total volume: 1240236.70
#   Average radius: 4.990
#   Cylinder radius: 4.959
#   Bounding box volume: 681182790

net.save(save_steps=True)
# Qiber3D_core [INFO] Network saved to Exp190309_PrMECs-NPF180_gel4_ROI-c.qiber

net.render.show()
net.render.compare()
```

A more extensive interactive example is available as a Jupyter notebook.
You can try it out directly on [Binder](https://mybinder.org/v2/gh/theia-dev/Qiber3D_jupyter/main?urlpath=git-pull%3Frepo%3Dhttps%253A%252F%252Fgithub.com%252Ftheia-dev%252FQiber3D%26urlpath%3Dtree%252FQiber3D%252Fdocs%252Fjupyter%252Findex.ipynb).
More in-depth documentation, including details on the inner working, can be found at [Read the docs](https://Qiber3D.readthedocs.io).


The complete source code is available on [GitHub](https://github.com/theia-dev/Qiber3D).


