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The FARSIGHT 3-D Trace Editor

From a biological image, tubular objects such as blood vessels and neurites can be represented by a series of cylinders. The centerlines of the cylinders can be represented by a series of 3-D points. By providing information about the connections between points the tree structure can be traced and stored in a data structure. The FARSIGHT 3-D Trace Editor is designed to provide a streamlined platform for multi-view visualization and Edit-based Validation System(EVS) for automatic neurite and vessel tracing algorithms. The Actively Linked Integrated Spaces Architecture (ALISA) manipulates multiple views and allows for the simplification 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 is possible using ALISA, as pattern analysis and clustering can aid in selection. The primary view in the editor is the 3D rendering which has the capability to display the traces as color coded lines with an overlay of a volume rendering from original image. The rendering can be viewed from any angle and at any desired magnification. The secondary display is the linked space where computed features can be displayed simultaneously in table and scatter plot form. The table and plot views can filter and sort the features simplifying selections which are automatically updated in all views. The group and automated functions provide an efficient method for validating complex data sets.

Image showing the editor Linked space displaying dendritic spines data.

Since the traces are represented as a sequence of points in 3-D space, they have a sense (directionality). Many automatic tracing algorithms produce a collection of trace fragments (segments) that don't have a consistent set of directions (sense). The trace editor is designed to cope with this challenge. It is also designed to allow "group editing". Using the linked space, you can select multiple segments at once, and perform an edit operation over the selected set of segments.

This screen shot illustrates the tool's ability to display secondary neuronal structures such as spines. The light blue traces correspond to the dendritic backbone, and the dark blue lines are the dendritic splines. The traces highlighted in orange are the selected traces. The small spheres indicate the spine bases.	This is another view of the linked space of the spines showing the features in a scatter plot allowing comparisons of traces using two features at a time.
This view in the linked space shows the spines' features in table form. Additional features loaded in through the RPIxml file can also be displayed.

How to run the trace editor:

This window will load a file to the Raycaster. This is good for showing original Image data.

When you double click on the Trace Editor Icon a dialog will appear asking for user information and initial files to open. The files include an acceptable tracing format, and image. Trace Editor can load additional files through the file menu while running. There are two rendering options for the input images; A Raycaster is used for a more detailed image such as the initial image. The Contour Filter, for displaying segmented images, such as somas, as a volume. Currently Trace Editor accepts the following file types as input:

Trace Files:
- .swc
- xml (RPI format)
- .vtk (this is only the 3D structure)

Image Files:
- tif
- pic

Trace Project
- .xml

Trace Project

The Trace Project is a xml document that tells the trace editor where to find multiple input files. The Project file loads information such as file type, and translation coordinates to tile multiple files into a montage. The following code is an example of an image translated so that it registers to the trace loaded.

<?xml version="1.0" ?>
<Source>
 <File FileName="C:\Lab\Traces\NC\Neocortical_Axons_01.tif" Type="Image" tX="73" tY="507" tZ="-5"/>
 <File FileName="C:\Lab\Traces\NC\NC_01.swc" Type="Trace" tX="0" tY="0" tZ="0"/>
</Source>

Some Information on the project file
- File Name:
  - Needs to Include the Path Such as C:\Lab\Traces\NC\
- Type:
  - "Image" Original Image Data
  - "Soma" Segmented Image of the Cell Body
  - "Trace" Any Valid Trace File

The results can show the Traces displayed as lines, and the original image as a 3D volume with adjustable brightness and opacity. This allows for validation of the traces, and a more intuitive way to visualization of the data than 2D slices or table formats. In addition to being able to display the original image, the Trace Editor can also display segmented soma images. This data is also rendered in 3D and then overlaid on the traces. Rendering the somas along with the traces allows for more accurate validation. The increased accuracy enables greater ease in associating processes with the proper soma and also in correcting and validating the directionality of the processes.

Trace lines, the original image (in red), and the somas (in blue) all rendered together. The Image has been annotated to show different aspects of the Editors display capabilities.

Usage

Once the Trace Editor has successfully launched, the render window will have interactive 3-D viewing and editing capabilities. Several operations have automated and semi-automated functionality depending upon the input. For manual selective editing, you can point the computer mouse and highlight a series trace segments of by right clicking them(shown by selectable color). The editing operations are grouped by functions in the following categories of selection, modification, and settings.

Selection operations,

for controlling which traces are modified:

Automatic 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 "-") removes the last selected line, color will revert to original when next pick is selected.

Trace Modification Operations,

for changing trace structure:

Delete 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:

operating in one of three modes it will attempt to merge traces based on selection inputs. The first time pressed it will determine and save all the comparisons for selection, and on second press will merge all selected comparisons.
(Hot Key "m")

Two Traces selected: If a merge is possible under the current tolerance it will be merged.
Multiple Traces Selected: All probable merges will be made based on selected lines and current tolerance.
Null Selection: If there are no currently selected lines all possible merges will be made from the entire trace structure.

Branch Point:

Adds a children to a parent trace, creating a new branch point. The tree structure will be modified to reflect the change.
(Hot Key "b") Defines a parent as the first Trace selected and children as all following selections

Flip Trace Direction:

Flip the direction of the selected trace lines and update the rest of the tree consistently.

Settings

adjust global parameters:

Tolerances: adjust the following rendering and threshold functions:

Gap 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 to help with visibility when displaying on screen.

Apply edit settings

Load Soma:

Opens a dialog to find a soma image (tiff, PIC) and render it.

Complex Edit Operations

Note that the functions listed above are designed to handle multiple segments at a time. The MinEndPoints function determines the closest distances between trace endpoints, distances greater than the threshold are rejected. For detailed information on the features used in computation please see Trace Editor/Features. Conflicts between two lines attempting to connect to one endpoint are resolved by finding the closest endpoints. The merge command can be invoked on a set of traces, and this function will automatically connect all the possible segments. Multiple tracelines can be orginized and merged into a single linear trace.

This animation walks through how the merge operation can proceed for a semi-automated group editing. The computer automatically selects tracing candidates that the user can refine the selection.

Trace Editor