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Code accompanying the manuscript "In-vivo quantitative image analysis of age-related morphological changes of C. elegans neurons reveals a correlation between neurite bending and novel neurite outgrowths" of Hess et al.
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images
.gitignore
LICENCE.txt
README.md
batchProcessing.py
beads.py
classify.py
cleanup.py
kinkPositions.py
requirements.txt
somaVolume.py
utility.py
wavyness.py

README.md

NeuronMorphologyQuantification

Code accompanying the manuscript "In-vivo quantitative image analysis of age-related morphological changes of C. elegans neurons reveals a correlation between neurite bending and novel neurite outgrowths" by Hess et al. https://doi.org/10.1523/ENEURO.0014-19.2019

Data

You can download the full dataset from Zenodo.

NeuronMorphologyQuantificationData
├── ALM
│   ├── images
|   │   ├── CONDITION_AGE_SERIES_NAME.tif
|   │   └── ...
│   └── trees
|       ├── CONDITION_AGE_SERIES_NAME.swc
|       └── ...
└── PLM
    ├── images
    │   ├── CONDITION_AGE_SERIES_NAME.tif
    │   └── ...
    └── trees
        ├── CONDITION_AGE_SERIES_NAME.swc
        └── ...

Preprocessed images can be found in the 'images' folder. The 'trees' folders contain neuron tracings from the APP2 algorithm with manual annotations.

Requirements

  • Python 3.6
  • The following python packages*
    • numpy 1.16.2
    • matplotlib 3.0.3
    • scipy 1.2.1
    • scikit-image 0.15.0
    • SimpleITK 1.2.0
    • tqdm 4.31.1

*All these packages can be automatically installed with pip by running python -m pip install -r requirements.txt on the code directory

Instructions

  1. Clone the repository and download the full data from Zenodo
  2. In batchProcessing.py set the parameter root to the directory containing the data
  3. Run the script batchProcessing.py

Output

Measurement Files:

  • root/yyyy-mm-dd_hh-mm-ss_IndividualMeasurements.csv
    Contains individual length measurements of structures (i. e. soma-outgrowths)
  • root/yyyy-mm-dd_hh-mm-ss_SummaryMeasurements.csv
    Contains mesaruements corresponding to individual neurons (i. e. sharp-bend counts)
  • root/yyyy-mm-dd_hh-mm-ss_Parameters.txt
    Contains a copy of the parameters used

Visualizations

  • root/(ALM|PLM)/classifiedtrees/
    This folder contains .swc files with classified nodes.
  • root/(ALM|PLM)/wavytrees/
    This folder contains .swc files with sharp bends and beads visualised.

You can use software like neuTube to visualize the results.

Internal use of the .swc format

General

The .swc format allows representation tree structures and is the most common output format of neuron tracing algorithms. The following table contains an example of four connected nodes and a corresponding visualization.

Index Type X Y Z Radius Parent
1 0 0 0 0 1 -1
2 0 3 2 0 1 1
3 0 4 3 0 1 2
4 0 4 1 0 1 2

We use .swc files in this work as (1) input trees (neuron tracing output with manual annotations), to (2) visualize the results of our classification and to (3) visualize the quantification of kinks and bends. Neuronal trees are internally represented as numpy.ndarrays of shape (7, n_nodes).

Input Annotations

Our pipeline expects .swc files with the types of all nodes set to 0. To annotate PVM-connections (PLM-sidebranches that connect to the PVM neuron that cannot be differentiated from neurite-outgrowths) set the types of one or more of their nodes to 1 or 2. If a crossing PVM process is not properly detected as such you can annotate it by setting one or more nodes to 3.

Output Annotations

Classification

Classified neuron trees (../classifiedtrees) have the following naming convention:

Structure Type Description
Soma node 0 Beloning to soma.
Mainbranch 1 Belonging to main branch.
Neurite outgrowth 2 Belonging to process sprouting from main branch.
Soma outgrowth 3 Belonging to process sprouting from soma node.
Blob 5 Sharp bend in process that is not an outgrowth event.
PVM-crossing 6 Process of PVM neuron that crosses the PLM neuron.
PVM-connection 7 Regular connection(s) (1-2) to PVM neurons (no branching event).
Unknown 9 None of the above.
Silenced outgrowth 10 Outgrowth event in the first or last segment of the mainbranch, silenced as in those regions a lot of tracing errors occur.

Wavyness

For the visualization of wavyness (../wavytrees/COND_AGE_SERIES_NAME.swc) the radii of all nodes of the mainbranch are set to 0.5. The type of a node corresponts to the mapping of its angle (0-180 degrees) to an integer in the range 1-10 inclusive. The radii of nodes detected as sharp bends are set to 3.

Beads

Visualization of beads (../wavytrees/COND_AGE_SERIES_NAME_beads.swc) is done by doubling the radius of the bead-nodes and setting their type to 1.

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