IVE Applications Listed by Purpose

IVE applications are listed below by what they do. If online help is available, the application name appearing before the description is a link to the help file.

Automatic segmentation

2DObjFinder

Finds the polygons that bound the regions of a binary image (has data values of zero and one only).

EditPolygon

Has options for interactively or automatically generating polygonal models from the data in an image window.

FPPolygons

Is similar to 2DObjFinder with the option to associate the polygons into three dimensional volumes.

Tracer

Can trace the axis of a tube-like structure.

Color

BlendColors

Blends multiple wavelength data to form an RGB image.

ChangeColors

Changes the 12 colors available for use in graphics overlayed on images.

SelectGrColors

Is a monitor function to select precedence for the 12 colors used to draw graphics on top of the image.

SelectImgColors

Is a monitor function to toggle pseudocolor and true color display and to colors used to draw each image wavelength.

Conversion

CopyRegion

Copies (with the option to convert the data type) a rectangular subset of data from a file or window to another file or window.

ImgToMat

Converts from Priism's native format to a MATLAB workspace file (.mat).

MatToImg

Converts a MATLAB workspace file (.mat) to Priism's native format.

mergemrc

Is a command line utility (mergemrc) or application with a graphical interface (mergemrc_i) to combine or reorder IVE image data files.

Mrc2tiff

Converts Priism's native format into TIFF.

Mrc2txt

Converts Priism's native image format into text.

PickToModel

Generates a 3D model file from the output of PickPoints.

Tiff2mrc

Converts TIFF files into Priism's native format.

TiffMovie

Does a screen capture from a Priism image window to generate a sequence of TIFF files which can be used as input to a movie generating application like SGI's mediaconvert.

vaxmrc2mrc

Is a command line utility for converting IVE data written on a VAX.

VolumeBuilder

Assembles two-dimensional polygons into a three-dimensional model and can report some of the typical measurements for such a model.

Data views

2d_plot

Is a utility for 2D plotting from CURVY data files.

AppendRes

Appends lower resolution data sets to an existing file or window.

Flip

Rearranges the data to interchange one axis (x, y, z) for another.

Movie

Automates the process of moving through the sections in an image window.

Resample2D

Generates a resampled data set by some combination of shifting the origin, rotating the axes, or changing the pixel spacing.

rot3d

Provides most of the same capabilities as Rotate3D (i.e. to generate a view of a data set from an arbitrary angle or to do 3D resampling), but in a command-line interface.

Rotate3D

Generates a new data set from an existing data set seen from an arbitrary viewing angle. Also useful for resampling a dataset in 3 dimensions.

rotfast

Is a command line application to generate a projection series (2D views of the data set as it is rotated about the y axis).

RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent z sections from an existing data set to form a new data set.

Slider

Is a utility for simultaneously changing sections in all open image windows.

T-RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent time points from an existing data set to form a new data set.

volume

Is a command line utility for volume rendering.

VolumeViewer

Does interactive volume rendering (projects the data set to a 2D view).

EM Processing

Alignment File Manipulator

Is a command-line application (tfalignment) and a more limited interactive application (tfalignment_i) to convert the alignment parameters for a tilt series so that they are usable with a tilt series that is a resampled version of the original or only contains a subset of the tilts.

BALIGN (Bead Align)

Is a set of interactive and batch applications to identify beads in an EM tilt series and use them to calculate alignment parameters for reconstruction of a 3D data set.

Bead List Resample

Is a command-line application (tfbl) and an interactive application (tfbl_i) to convert the bead lists for a tilt series so that they are usable with a tilt series that is a subset or a resampled version of the original.

EMRECON (Reconstruction)

Is a set of batch applications to construct a 3D data set from an EM tilt series and a set of alignment parameters (typically calculated by BALIGN). The reconstruction package was significantly modified in the March 2000 release. The old version is available.

OldEMRECON (Reconstruction)

This is the version of EMRECON used prior to the March 2000 release. It is a set of batch applications to construct a 3D data set from an EM tilt series and a set of alignment parameters (typically calculated by BALIGN).

Enhancement

Convolution

Convolves the data (replaces each value with a linear combination of the surrounding values) with a two-dimensional kernel (the array of weights to use in the linear combination).

EdgeEnh

Applies a 3D edge enhancement operation to the data.

Filter2D

Applies one of a variety of two dimensional filters (mean, median, ...) to smooth or sharpen an image.

Filter3D

Applies a three dimensional local mean filter to the data to smooth it.

HisEqual

Performs a histogram equalization (a systematic alteration of the data values to obtain a data set whose values are uniformly distributed). The mapping is based on the distribution of data in each section; the LCE application is similar but uses local characteristics of the data.

LCE 2D

Performs a local contrast enhancement (a systematic alteration of data values based on a locally calculate distribution to obtain a user specified distribution).

LCE 3D

Functionally similar to LCE 2D but uses a three dimensional neighborhood to calculate the local mean and contrast values that are factors in the contrast enhancement.

NewConvolution

Is very similar to Convolution but removes restrictions on the size of the kernel.

Normalize

Linearly rescales each section of a data set so that each section has the same range of values.

Export/Import

ImgToMat

Converts from Priism's native format to a MATLAB workspace file (.mat).

MatToImg

Converts a MATLAB workspace file (.mat) to Priism's native format.

Mrc2tiff

Converts Priism's native format into TIFF.

Mrc2txt

Converts Priism's native image format into text.

Tiff2mrc

Converts TIFF files into Priism's native format.

TiffMovie

Does a screen capture from a Priism image window to generate a sequence of TIFF files which can be used as input to a movie generating application like SGI's mediaconvert.

vaxmrc2mrc

Is a command line utility for converting IVE data written on a VAX.

Fourier tools

ffilter

Applies a cylindrically symmetric two or three dimensional filter.

Filter2D(Fourier)

Applies a 2D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.

Filter3D(Fourier)

Applies a 3D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.

FPwrSpec2D

Calculates estimates of the 2D power spectra from the Fourier transform of the input with the option to average over multiple input blocks or smooth the final result.

FPwrSpec3D

Calculates estimates of the 3D power spectra from the Fourier transform of the input with the option to average over multiple input blocks or smooth the final result.

FTransform2D

Calculates a two-dimensional forward or reverse Fourier transform of the input.

FTransform3D

Calculates a three-dimensional forward or reverse Fourier transform of the input.

Fourier tools (old)

ButterFilters2D

Applies a 1st or 2nd order Butterworth filter (low- or high- pass) to each section in the input. In newer versions of Priism, use Filter2D (Fourier) instead.

ButterFilters3D

Applies a 1st or 2nd order Butterworth filter (low- or high- pass). In newer versions of Priism, use Filter3D (Fourier) instead.

FourierTransf2D

Generates the logarithm of the magnitude of the two-dimensional transform of each input section. In newer versions of Priism, consider using FTransform2D or FPwrSpec2D instead.

FourierTransf3D

Generates the logarithm of the magnitude of the three-dimensional transform. In newer versions of Priism, consider using FTransform3D or FPwrSpec3D instead.

GaborFilter2D

Applies a two-dimensional Gabor filter (specified in polar coordinates) to each input section. In newer versions of Priism, use Filter2D (Fourier) instead.

GaborFilter3D

Applies a three-dimensional Gabor filter (specified in spherical coordinates with the same width in all directions). In newer versions of Priism, use Filter3D (Fourier) instead.

GaussianFilter2D

Filters each section in the input with a radially symmetric filter that is the sum of two Gaussians. In newer versions of Priism, use Filter2D (Fourier) instead.

GaussianFilter3D

Filters the input with a radially symmetric filter that is the sum of two Gaussians. In newer versions of Priism, use Filter3D (Fourier) instead.

MeanPwrSpctrm2D

Is similar to PowerSpectrum2D but the input can be broken into several parts, several power spectra calculated, and the average result returned. For newer versions of Priism, consider using FPwrSpec2D instead.

MeanPwrSpctrm3D

Is similar to PowerSpectrum3D but the input can be broken into several parts, several power spectra calculated, and the average result returned. For newer versions of Priism, consider using FPwrSpec3D instead.

PowerSpectrum2D

Generates the logarithm of the power spectrum for each input section (with the option to generate radial power spectra as well). For newer versions of Priism, consider using FPwrSpec2D instead.

PowerSpectrum3D

Generates the logarithm of the power spectrum (with the option to generate radial power spectrum as well). For newer versions of Priism, consider using FPwrSpec3D instead.

Image information

EditHeader

Displays and allows the editing of the image data header of a file or window.

ExamineData

Displays the data as a spreadsheet like table.

Line Profile

Draws a plot of intensity for a cross-section of a data set on top of an image window. Also does a rough calculation of full-width at half maximum (FWHM) for peak values.

Point

Displays the data value and scaled image value corresponding to the location of the mouse pointer.

Region MMM

Calculates the min, max, and mean of one or more selected regions of a data set.

Image window

CopyRegion

Copies (with the option to convert the data type) a rectangular subset of data from a file or window to another file or window.

DisplayAttr

Is a monitor function to edit an image window's characteristics.

ImageInfo

Is a monitor function to display and edit the image data header.

MeasureFPS

Reports the redraw rate for an image window.

Monitor

Manages an image window.

Movie

Automates the process of moving through the sections in an image window.

Scale

Is a monitor function to adjust the image scaling and show the image histogram.

SelectGrColors

Is a monitor function to select precedence for the 12 colors used to draw graphics on top of the image.

SelectImgColors

Is a monitor function to toggle pseudocolor and true color display and to colors used to draw each image wavelength.

Slider

Is a utility for simultaneously changing sections in all open image windows.

ViewFile

Opens an image window which is attached to a disk file.

Interactive segmentation

3DModel

Is an application to view, edit, and make measurements of three dimensional models.

EditPolygon

Has options for interactively or automatically generating polygonal models from the data in an image window.

PickPoints

Allows you to interactively select points from an image window. The generated list of points can be used with PickToModel or in the automatic polygon construction functions in EditPolygon.

Masking

2DObjFinder

Finds the polygons that bound the regions of a binary image (has data values of zero and one only).

CutMask

Masks an input file using polygon data.

FindBorder

Generates a data set where the borders of regions above a fixed threshold are set to one. The remainder of the data set is filled with zeroes.

FindPoints

Has several more or less sophisticated methods for selecting points from a data set.

FPPolygons

Is similar to 2DObjFinder with the option to associate the polygons into three dimensional volumes.

RegionGrowing

Given a list of points, identifies regions about those points based on a threshold criteria.

Straight

Cuts out a tube of data about the points specified in a model file.

Threshold

Creates a new data set where the values at points which were below a fixed threshold are set to a constant value (typically zero) and the values at points above a fixed threshold are either preserved or set to another fixed value (typically one). A list of the points above the threshold can also be created.

Watershed

Implements a watershed segmentation algorithm.

Measurement

3DModel

Is an application to view, edit, and make measurements of three dimensional models.

Clouds

Performs distance measurements between point(s) in one model and point(s) in the same model or another model.

Distance

Calculates distances between points selected in an image window.

Line Profile

Draws a plot of intensity for a cross-section of a data set on top of an image window. Also does a rough calculation of full-width at half maximum (FWHM) for peak values.

Region MMM

Calculates the min, max, and mean of one or more selected regions of a data set.

VolumeBuilder

Assembles two-dimensional polygons into a three-dimensional model and can report some of the typical measurements for such a model.

Model file conversion

PickToModel

Generates a 3D model file from the output of PickPoints.

SurfHarmMod

Takes a model file (one appropriate for use with 3DModel) and fits the objects in the model with spherical harmonic expansions.

VolumeBuilder

Assembles two-dimensional polygons into a three-dimensional model and can report some of the typical measurements for such a model.

Model usage

Clouds

Performs distance measurements between point(s) in one model and point(s) in the same model or another model.

CutMask

Masks an input file using polygon data.

FindPoints

Has several more or less sophisticated methods for selecting points from a data set.

Straight

Cuts out a tube of data about the points specified in a model file.

Modeling

2DObjFinder

Finds the polygons that bound the regions of a binary image (has data values of zero and one only).

3DModel

Is an application to view, edit, and make measurements of three dimensional models.

EditPolygon

Has options for interactively or automatically generating polygonal models from the data in an image window.

FindPoints

Has several more or less sophisticated methods for selecting points from a data set.

FPPolygons

Is similar to 2DObjFinder with the option to associate the polygons into three dimensional volumes.

PickPoints

Allows you to interactively select points from an image window. The generated list of points can be used with PickToModel or in the automatic polygon construction functions in EditPolygon.

PickToModel

Generates a 3D model file from the output of PickPoints.

RegionGrowing

Given a list of points, identifies regions about those points based on a threshold criteria.

SurfHarmMod

Takes a model file (one appropriate for use with 3DModel) and fits the objects in the model with spherical harmonic expansions.

Threshold

Creates a new data set where the values at points which were below a fixed threshold are set to a constant value (typically zero) and the values at points above a fixed threshold are either preserved or set to another fixed value (typically one). A list of the points above the threshold can also be created.

Tracer

Can trace the axis of a tube-like structure.

VolumeBuilder

Assembles two-dimensional polygons into a three-dimensional model and can report some of the typical measurements for such a model.

Watershed

Implements a watershed segmentation algorithm.

Motion

Movie

Automates the process of moving through the sections in an image window.

Slider

Is a utility for simultaneously changing sections in all open image windows.

Not in Priism menus

Combine

Is a command line utility for merging IVE image data files. In newer versions of Priism, use mergemrc which handles a broader range of situations than Combine does.

pf2psf

Computes slices through the point spread function (PSF) from an image of the pupil function.

pffit

Fits Zernike polynomials to a pupil function image.

pfimage

Computes a pupil function image from a parametric description of the pupil function.

phretavr

Retrieves an image of the pupil function from a series of z slices through the point spread funcion.

radialft_asym

Radially averages the 3D Fourier transform of a point source to generate a CTF for deconvolution.

rot3d

Provides most of the same capabilities as Rotate3D (i.e. to generate a view of a data set from an arbitrary angle or to do 3D resampling), but in a command-line interface.

simplex

Is a command line application to align multiple wavelength data.

superimpose_psf

Performs several steps (combining of multiple exposures, peak position determination, estimation and subtraction of background) commonly needed when converting an image of a bead to a CTF for deconvolution.

vaxmrc2mrc

Is a command line utility for converting IVE data written on a VAX.

volume

Is a command line utility for volume rendering.

OM Processing

applycal

Is a command line utility (applycal_i is a graphical front-end) to apply a calibration file and edit bad pixels in a data set if those operations were not done during data collection.

CCDCor

Corrects optical microscopy data for variations in illumination and photobleaching. Can also attempt to identify CCD irregularities and replace the affected areas with interpolated values.

Decon

Performs an iterative two- or three- dimensional deconvolution to increase the resolution of the data by removing out-of-focus light and blurring effects due to the optics.

FixBadPixel

Uses a bad pixel list generated by Resolve3D and applies it to a data set to interpolate the data values at bad pixels.

pf2psf

Computes slices through the point spread function (PSF) from an image of the pupil function.

pffit

Fits Zernike polynomials to a pupil function image.

pfimage

Computes a pupil function image from a parametric description of the pupil function.

phretavr

Retrieves an image of the pupil function from a series of z slices through the point spread funcion.

radialft_asym

Radially averages the 3D Fourier transform of a point source to generate a CTF for deconvolution.

superimpose_psf

Performs several steps (combining of multiple exposures, peak position determination, estimation and subtraction of background) commonly needed when converting an image of a bead to a CTF for deconvolution.

Plotting

2d_plot

Is a utility for 2D plotting from CURVY data files.

Line Profile

Draws a plot of intensity for a cross-section of a data set on top of an image window. Also does a rough calculation of full-width at half maximum (FWHM) for peak values.

Processing

ButterFilters2D

Applies a 1st or 2nd order Butterworth filter (low- or high- pass) to each section in the input. In newer versions of Priism, use Filter2D (Fourier) instead.

ButterFilters3D

Applies a 1st or 2nd order Butterworth filter (low- or high- pass). In newer versions of Priism, use Filter3D (Fourier) instead.

Combine

Is a command line utility for merging IVE image data files. In newer versions of Priism, use mergemrc which handles a broader range of situations than Combine does.

Convolution

Convolves the data (replaces each value with a linear combination of the surrounding values) with a two-dimensional kernel (the array of weights to use in the linear combination).

CopyRegion

Copies (with the option to convert the data type) a rectangular subset of data from a file or window to another file or window.

EdgeEnh

Applies a 3D edge enhancement operation to the data.

ffilter

Applies a cylindrically symmetric two or three dimensional filter.

Filter2D

Applies one of a variety of two dimensional filters (mean, median, ...) to smooth or sharpen an image.

Filter2D(Fourier)

Applies a 2D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.

Filter3D

Applies a three dimensional local mean filter to the data to smooth it.

Filter3D(Fourier)

Applies a 3D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.

GaborFilter2D

Applies a two-dimensional Gabor filter (specified in polar coordinates) to each input section. In newer versions of Priism, use Filter2D (Fourier) instead.

GaborFilter3D

Applies a three-dimensional Gabor filter (specified in spherical coordinates with the same width in all directions). In newer versions of Priism, use Filter3D (Fourier) instead.

GaussianFilter2D

Filters each section in the input with a radially symmetric filter that is the sum of two Gaussians. In newer versions of Priism, use Filter2D (Fourier) instead.

GaussianFilter3D

Filters the input with a radially symmetric filter that is the sum of two Gaussians. In newer versions of Priism, use Filter3D (Fourier) instead.

HisEqual

Performs a histogram equalization (a systematic alteration of the data values to obtain a data set whose values are uniformly distributed). The mapping is based on the distribution of data in each section; the LCE application is similar but uses local characteristics of the data.

ImageArith

Is a utility for adding, subtracting, multiplying, dividing, or scaling data sets.

LCE 2D

Performs a local contrast enhancement (a systematic alteration of data values based on a locally calculate distribution to obtain a user specified distribution).

LCE 3D

Functionally similar to LCE 2D but uses a three dimensional neighborhood to calculate the local mean and contrast values that are factors in the contrast enhancement.

mergemrc

Is a command line utility (mergemrc) or application with a graphical interface (mergemrc_i) to combine or reorder IVE image data files.

NewConvolution

Is very similar to Convolution but removes restrictions on the size of the kernel.

Normalize

Linearly rescales each section of a data set so that each section has the same range of values.

RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent z sections from an existing data set to form a new data set.

simplex

Is a command line application to align multiple wavelength data.

T-RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent time points from an existing data set to form a new data set.

Projection

rotfast

Is a command line application to generate a projection series (2D views of the data set as it is rotated about the y axis).

RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent z sections from an existing data set to form a new data set.

T-RunProj

Combines (by taking a sum, average, or maximum) one or more adjacent time points from an existing data set to form a new data set.

volume

Is a command line utility for volume rendering.

VolumeViewer

Does interactive volume rendering (projects the data set to a 2D view).

Resolution

AppendRes

Appends lower resolution data sets to an existing file or window.

ReduceRes

Produces a reduced resolution data set by averaging over adjacent pixels.

Resample2D

Generates a resampled data set by some combination of shifting the origin, rotating the axes, or changing the pixel spacing.

Rotate3D

Generates a new data set from an existing data set seen from an arbitrary viewing angle. Also useful for resampling a dataset in 3 dimensions.

Rotation

Flip

Rearranges the data to interchange one axis (x, y, z) for another.

rot3d

Provides most of the same capabilities as Rotate3D (i.e. to generate a view of a data set from an arbitrary angle or to do 3D resampling), but in a command-line interface.

Rotate3D

Generates a new data set from an existing data set seen from an arbitrary viewing angle. Also useful for resampling a dataset in 3 dimensions.

rotfast

Is a command line application to generate a projection series (2D views of the data set as it is rotated about the y axis).

volume

Is a command line utility for volume rendering.

VolumeViewer

Does interactive volume rendering (projects the data set to a 2D view).

modified March 19, 2004