Seg3D Pages

Web pages for Seg3D

View the Project on GitHub SCIInstitute/Seg3D

Seg3d Tools

There are many different tools and filters implemented in Seg3D. These tools and filters are there to attempt several tasks, from reformatting original data, smoothing and de-noising image data, to automatic and manual segmenting. Every tool and filter will be describe briefly in an effort to provide the user with a list of methods that may be used to segment the data that they have. These methods have been separated into four categories, general tools, mask filters, data filters, and advanced filters.

Most of the tools and filters have a ‘replace’ option. The default for most of these functions is to create a new layer, but ‘replace’ will cause the new layer to instead replace the old one. This is very useful in avoiding the generation of multiple layer that are only intermediate steps. Also, most tools and filters will by default insert the active layer as the primary input. You may disable this and choose manually which layer to modify.

Many of the tools and filters must use a certain type of data as the input, either mask or image data. If the wrong type of layer is chosen as the input, the tool/filter interface will display a warning message in a red box near the execution button informing you of this. The tool will also be disabled until the correct type of layer is chosen. This second feature applies to empty inputs also.

A final note is that when tools have multiple inputs, the inputs must all be from the same layer group (geometric grid), with exception of the registration tool. This ensures that all the voxels in the multiple inputs have corresponding voxels to every other input volume.

AdvancedFilters

CannyEdge

ConfidenceConnected

CurvatureAnisotropicDiffusion

DistanceMap

GradientAnisotropicDiffusion

GradientMagnitude

HistogramEqualization

IntensityCorrection

SegmentationLevelSet

DataFilters

Arithmetic

GaussianBlur

MaskData

Mean

Median

NeighborhoodConnected

OtsuThreshold

LargeVolumeTools

ExtractDataLayers

MaskFilters

BooleanAND

BooleanOR

BooleanRemove

ConnectedComponentSize

ConnectedComponent

FastBinaryDilateErode

FillHoles

SmoothBinaryDilateErode

Tools

CopyPaste

Crop

FlipRotate

ImplicitModel

Invert

Measure

Pad

PaintBrush

PointSetRegister

Polyline

Resample

SelectPoints

Speedline

Threshold

Transform