• Which structure can cause disorder?

• What is the most affective factor?

▲ A. J. Billnitzer, et al. (2013)

APP independent and dependent effects on neurite outgrowth

are modulated by the receptor associated protein (RAP)

▲ Halavi M, Hamilton KA, Parekh R, Ascoli GA. (2012)

Digital reconstructions of neuronal morphology: three decades of research trends

Method

Sholl Analysis NeuronJ NeuriteTracer

Approach Counting distance boundary Manual tracing (path finding) Convolution skeletonize

Published 1953 2004 2008

Average time cost - More than 1 min. 0.3~0.5 seconds

Major Limitation Indirect measurement Time & handling cost Total length/Image only

▲ AM. Magariños et al. (2006)

Method by D. A. Sholl, (1953)

▲ M. Pool, et al. (2008)▲ E. Meijering et al. (2004)

1.

2.

3.

↓ Loading

↓ Thresholding

↓ Sampling

↓ Modeling

↓ Structuring

↓ Measuring

A Pixel = The smallest controllable

element of a picture represented

on the screen.

(http://en.wikipedia.org/wiki/Pixel)

↓ Thresholding

↓ Sampling

↓ Modeling

↓ Structuring

▼ K.Srinivas, V. Srikanth, (2011)

Automatic histogram threshold with fuzzy measures using C-means

Computation

↓ Thresholding

↓ Sampling

↓ Modeling

↓ Structuring

↓ Thresholding

↓ Sampling

↓ Modeling

↓ Structuring

FixedMerged

▼ H. Huang, et al. (2013) L1-Medial skeleton of point cloud

↓ Thresholding

↓ Sampling

↓ Modeling

↓ Structuring

Sample Images - K. Fukumoto., Y. Gobayashi. 2012, Hiroshima University

- Primary culture of cortical neuron (ICR E15.5), α-GFP ICC, div3/9,

- Photos taken from FV1000 (Olympus, Japan)

- 8-bit monochrome TIF conversion through ImageJ custom plugin

(N=100 sample images)

Correlation coefficient (Pearson) by manual.

T4trace showed about 10% higher score

than NeuriteTracer

(N=100 sample images)

High-throughput screening Large-scale Reconstruction

• Automatic thresholding: K.Srinivas, V. Srikanth, (2011) Automatic histogram threshold with fuzzy measures using C-means

• L-median skeletonize: H. Huang, et al. (2013) L1-Medial skeleton of point cloud

• Page 2. A. J. Billnitzer, et al. (2013) APP independent and dependent effects on neurite outgrowth are modulated by the receptor

associated protein (RAP)

• Page 3. M. Halavi, et al. (2012) Digital reconstructions of neuronal morphology: three decades of research trends.

• Page 4. (Left) AM. Magariños et al. (2006) Rapid and reversible changes in intrahippocampal connectivity during the course of

hibernation in European hamsters

• Page 4. (Right) M . Pool, et al., (2008) NeuriteTracer: A novel ImageJ plugin for automated quantification of neurite outgrowth

• Page 16. (Left) http://en.wikipedia.org/wiki/Sanford-Burnham_Medical_Research_Institute

• Page 16. (Right) http://www.wired.co.uk/magazine/archive/2013/09/start/clear-thinking

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https://insaint03.github.io/t4trace

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