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The FARSIGHT Trace Editor: An Open Source Tool for 3-D Inspection and Efficient Pattern Analysis Aided Editing of Automated Neuronal Reconstructions

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Notes

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  6. The trace editor is part of the free and open source FARSIGHT toolkit for biological image analysis (www.farsight-toolkit.org)

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  16. Brown, K.M., Barrionuevo, G., Canty, A.J., De Paola, V., Hirsch, J.A., Jefferis, G.S.X.E., Lu, J., Snippe, M., Sugihara, I., & Ascoli, G.A. (2011). The DIADEM data sets: representative light microscopy images of neuronal morphology to advance automation of digital reconstructions. Neuroinformatics, doi:10.1007/s12021-010-9095-5

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Acknowledgements

This work was supported primarily by NIH grant R01 EB005157 and by NSF grants EEC-9986821. The authors thank the DIADEM organizers for conducting such a unique competition and the dataset providers for generously providing the data to work with. These datasets provided the much-needed impetus to advance the trace editing tools in FARSIGHT in new ways, especially the scalability needed to handle large datasets.

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Correspondence to Badrinath Roysam.

Appendix A: Feature Calculation

Appendix A: Feature Calculation

Intrinsic Features

  1. 1

    Trace ID:

    • The ID is a unique number to look up each trace

  2. 2

    Radius:

    • Average Radius of the Trace

  3. 3

    Type:

    • The type of neural structure it is

  4. 4

    Parent:

    • The ID of the previous Trace in the tree, -1 if it is a root

  5. 5

    Root ID:

    • The ID of the first trace of each tree

  6. 6

    Level:

    • Following the shortest path how many bifurcations in the tree to reach the root.

  7. 7

    Number of Children:

    • How many children branch from the trace

    • 0 or 2, if it is not a soma

  8. 8

    Leaf Node:

    • Determine if the Trace is a terminal tip

Computed Features

  1. 1

    # of Bits:

    • How many traced points in the segment

    • n

  2. 2

    Euclidian Length:

    • The length of a straight line fitted between two points

    • $$ D = \sqrt[2]{{{{\left( {{p_{{1,x}}} - {p_{{2,x}}}} \right)}^2} + {{\left( {{p_{{1,y}}} - {p_{{2,y}}}} \right)}^2} + {{\left( {{p_{{1,z}}} - {p_{{2,z}}}} \right)}^2}}} $$
  3. 3

    Path Length:

    • Summation of the Euclidian distance between bits

    • \( L = \sqrt[{\sum {_{{i = 0}}^{{n - {1^2}}}} }]{{{{\left( {{p_{{i,x}}} - {p_{{i + 1,x}}}} \right)}^2} + {{\left( {{p_{{i,y}}} - {p_{{i + 1,y}}}} \right)}^2} + {{\left( {{p_{{i,z}}} - {p_{{1,z}}}} \right)}^2}}} \)

  4. 4

    Fragmentation Smoothness:

    • Ratio of path length to Euclidian distance

    • \( s = \frac{L}{D} \)

  5. 5

    Trace Density:

    • The average spacing between traced points

    • \( \frac{L}{n} \)

  6. 6

    Volume:

    • Calculates as a sum of cylinders along the path

    • \( V = \sum {_0^{{n - 1}}\pi {{\left( {{r_i}} \right)}^2}*Di,i + 1} \)

  7. 7

    Distance to Parent:

    • Euclidian distance between parent and child end points

  8. 8

    Path to Root:

    • Summation of the path length and distance to parent

Features specific for merging

  1. 1

    Gap Size:

    • Minimum Distance between the endpoints of two traces

    • \( d = \sqrt[2]{{{{\left( {{x_1} - {x_2}} \right)}^2} + {{\left( {{y_1} - {y_2}} \right)}^2} + {{\left( {{z_1} - {z_2}} \right)}^2}}} \)

  2. 2

    Gap Angle:

    • Angle between two traces represented as normalized vectors

    • \( \theta = {\cos^{{ - 1}}}\left( {\frac{{{v_1}*{v_2}}}{{|{v_1}||{v_2}|}}} \right) \)

  3. 3

    Maximum Gap Distance:

    • User parameter to set maximum gap size

  4. 4

    Merging Cost:

    • Function for determining merging probability

    • \( C = \theta \left[ { \frac{d}{\Delta } } \right]s \)

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Luisi, J., Narayanaswamy, A., Galbreath, Z. et al. The FARSIGHT Trace Editor: An Open Source Tool for 3-D Inspection and Efficient Pattern Analysis Aided Editing of Automated Neuronal Reconstructions. Neuroinform 9, 305–315 (2011). https://doi.org/10.1007/s12021-011-9115-0

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