ReferencesASCOLI, GIORGIO and REBECCA GOLDIN. "Coordinate Systems for Dendritic Spines:A

Somatocentric Approach." John Wiley & Sons, Inc (1997).

Ascoli, Giorgio, et al. "Generation, description and storage of dendritic morphology data." Philosophical Transactions: Biological Sciences 356.1412 (2001): 1131-1145.

He, Wenyun, et al. "Automated Three-Dimensional Tracing of Neurons." Microscopy AND Microanalysis(2003).

www.farsight-toolkit.org/wiki/Trace_Editor

The FARSIGHT 3-D Trace Editor

R1

R2

Overview of the Strategic Research Plan

FundamentalScience

ValidatingTestBEDs

L1

L2

L3

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S1 S4 S5S3S2

Bio-Med Enviro-Civil

Jonathan Luisi, Arunachalam Narayanswamy, Zach Galbreth, Badrinath Roysam

Rensselaer Polytechnic Institute

Gordon-CenSSIS is a National Science Foundation Engineering Research Center supported in part by the Engineering Research Centers Program of the National Science Foundation (Award # EEC-9986821)

The Trace editor is built in C++ using Libraries from Kitware including:

ITK (insight toolkit)

VTK(Visualization ToolKit)

3-D Graphics

Cmake to compile

QT to create the GUI

3D Source Image

.tiff

.PIC

.raw

Tracing

FTL3D

RPI Trace 3D

MDL

Post Processing

Spine Ring

Connect to Somas

Edit Based Validation

Linked Space

Features

SelectAutomatic Selection:

•Selects lines based on criteria, currently selecting only small lines and allowing deletion.

• (Hot Key "A")

List Selection:

•Displays information about the currently selected trace lines.

• (Hot Key "l")

Clear Selection:

•Deselect all currently highlighted lines.

• (Hot Key "c")

• ( Hot key "-“)

ModifyDelete Trace:

•Removes all selected trace segments.

• (Hot Key "d")

Split Trace:

•Split each selected trace line into two parts, separating them at the point that they were selected.

• (Hot Key "s")

Merge Traces:

•Attempt to merge traces based on selection inputs.

•Uses ALISA

• (Hot Key "m").

Branch Point:

•Creates a new branch point.

•Parent Trace selected and children following

• (Hot Key "b")

Flip Trace Direction:

•Flip the direction of the selected trace lines

• (Hot Key “f")

SettingsGap tolerance:

•The fraction of the length of the lines allowable for merging.

Gap max:

• the maximum distance between endpoints allowed for merging.

Small line:

• threshold for what is considered a fragment, or small line to be deleted.

Selection color:

•Change the highlight color for selected lines.

Line width:

•Adjustment for the width of rendered lines

Apply edit settings

•Updates the current settings

FilesLoad Trace:

•Loads Supported trace Files

Load Image:

•Opens a source image (tiff, PIC) and render it (Ray Caster)

Load Soma:

•Opens a soma image (tiff, PIC) and render it (contour filter)

Abstract

From a biological image, tubular objects such as blood vessels and neurites canbe represented by a series of cylinders. The centerlines of the cylinders can berepresented by a series of 3-D points. By providing information about theconnections between points the tree structure can be traced and stored in a datastructure. The FARSIGHT 3-D Trace Editor is designed to provide a streamlinedplatform for multi-view visualization and Edit-Based Validation System (EVS) forautomatic neurite and vessel tracing algorithms. The Actively Linked IntegratedSpaces Architecture (ALISA) manipulates multiple views and allows for thesimplification of the display and subset selection of data, such as a 3D rendering,tables, or scatter plots. Group and automated editing of the trace structure ispossible using ALISA, as pattern analysis and clustering can aid in selection. Theprimary view in the editor is the 3D rendering which has the capability to displaythe traces as color coded lines with an overlay of a volume rendering from originalimage. The rendering can be viewed from any angle and at any desiredmagnification. The secondary display is the linked space where computedfeatures can be displayed simultaneously in table and scatter plot form. The tableand plot views can filter and sort the features simplifying selections which areautomatically updated in all views. The group and automated functions provide anefficient method for validating complex data sets.

Tracing Process

Table ViewColumn headers are the

Feature names

Rows corresponds to an unique object

Filter Data for feature values that fall within a range

Sort Data by the data in a column

Plot ViewVisualization of data

Comparison of clustering of one feature by another

Lasso selection of clusters

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L1

d

θ

• Gap sized

• Angle between tracesθ

• Total path lengthL

• Total Euclidian DistanceD

• Fragmentation smoothness S

• Maximum distance for mergeDelta

Merging Equations

Smart Editing

The Trace editor can automate several tasks such as merging fragmentedtraces into a continuous trace. The computer automatically can identify andrank the probability that two traces can be merged. This function can berun on user selected traces, or the entire dataset. The Linked Space allowsthe user to filter out ‘bad’ merges based on the calculated features. Withthis method the user can quickly and accurately validate large sets of data.When viewing the potential merges in multiple views patterns becomeevident increasing the confidence of the editing. The future is to fullyautomate the process using pattern recognition software to identify clustersin the data.

Patterns in the features show

good candidates for merging

in a cluster, and bad merges

in the outliers