IVE applications are listed below alphabetically. If online help is available, links to sources of information are listed in parentheses after the application name.

Priism | Applications by category | Applications by name

- 2d_plot (HTML online help, text online help)
- Is a utility for 2D plotting from CURVY data files.
- 2DObjFinder (HTML online help, text online help)
- Finds the polygons that bound the regions of a binary image (has data values of zero and one only).
- 3DModel (HTML online help, text online help)
- Is an application to view, edit, and make measurements of three dimensional models.
- A. N. Diffusion (HTML online help, text online help)
- Perform 2D or 3D nonlinear anisotropic diffusion filtering.
- AddNoise (HTML online help, text online help)
- Adds Poisson or Gaussian noise to a data set.
- Align (HTML online help, text online help)
- Is a monitor function to manually offset different wavelengths to align them for image display.
- align_2d_p (HTML online help, text online help)
- align_2d_p takes a single-axis tomographic series and determines the set of coordinate transformations necessary to align the images in the series to each other. The Alignment + Reconstruction user interface in Priism can launch align_2d_p for you.
- align_2d_pi (HTML online help, text online help)
- Is a command-line application to align two tilt series to one another.
- Alignment File Manipulator (HTML online help, text online help)
- 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.
- AppendRes (HTML online help, text online help)
- Appends lower resolution data sets to an existing file or window.
- appl_prm (HTML online help, text online help)
- appl_prm takes a single-axis tomographic series and generates a new series with the intensity data scaled and interpolated according to a set of alignment and mass-normalization parameters. The Alignment + Reconstruction user interface in Priism can launch appl_prm for you.
- Apply Calibration (HTML online help, text online help)
- Is a command line utility (applycal; 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.

Priism | Applications by category | Applications by name

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- BALIGN (Bead Align) (HTML online help, text online help)
- 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 (HTML online help, text online help)
- 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.
- BlendColors (HTML online help, text online help)
- Blends multiple wavelength data to form an RGB image.
- bprm2imod (HTML online help, text online help)
- Converts Priism's tomography alignment parameters to files that IMod can handle.
- Byte (Mode 0) Conversion (HTML online help, text online help)
- Is a command line utility (mrcbyte) or graphical user interface for converting between signed and unsigned interpretations of 8-bit MRC data.

Priism | Applications by category | Applications by name

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- CCDCor (HTML online help, text help file)
- 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.
- ChangeColors (HTML online help, text online help)
- Changes the 12 colors available for use in graphics overlayed on images.
- Clouds (HTML online help, text online help)
- Performs distance measurements between point(s) in one model and point(s) in the same model or another model.
- 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 (HTML online help, text online help)
- Copies (with the option to convert the data type) a rectangular subset of data from a file or window to another file or window.
- core2_decon (HTML help file, text help file)
- Provides an implementation of Muthuvel Arigovindan's ER-Decon II algorithm for 3D deconvolution.
- core_decon (HTML help file, text help file)
- Provides an implementation of Muthuvel Arigovindan's ER-Decon I algorithm for 3D deconvolution.
- CutMask (HTML online help, text online help)
- Masks an input file using polygon data.

Priism | Applications by category | Applications by name

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- Decimate (HTML online help, text online help)
- Downsamples a data set.
- Decon (HTML help file, text help file)
- 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.
- DisplayAttr (HTML online help, text online help)
- Is a monitor function to edit an image window's characteristics.
- Distance (HTML online help, text online help)
- Calculates distances between points selected in an image window.

Priism | Applications by category | Applications by name

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- EdgeEnh (HTML online help, text online help)
- Applies a 3D edge enhancement operation to the data.
- EditHeader (HTML online help, text online help)
- Displays and allows the editing of the image data header of a file or window.
- EditHeader2 (HTML online help, text online help)
- Displays and allows the editing of the header for different variants of the MRC format.
- EditPolygon (HTML online help, text online help)
- Has options for interactively or automatically generating polygonal models from the data in an image window.
- emctfvis (HTML online help, text online help)
- Is an application for visualizing the transmission electron microscopy contrast transfer function.
- EMTAR (Alignment and reconstruction) (HTML online help, text online help)
- Is a set of batch applications to align a EM tomographic data set and reconstruct a 3D volume from the aligned data.
- EMTIAR (Iterative alignment and reconstruction) (HTML online help, text online help)
- Is a batch application to iteratively refine the alignment parameters and reconstruction for an EM tomographic data set.
- EMTIARGPU (Iterative alignment and reconstruction using GPUs) (HTML online help, text online help)
- Is a batch application to iteratively refine the alignment parameters and reconstruction for an EM tomographic data set. It uses servers with graphics cards to perform the reconstruction and projection calculations.
- ewbp (HTML online help, text online help)
- ewbp generates a 3D reconstruction from a single-axis tomographic series using a weighted backprojection algorithm. The Alignment + Reconstruction user interface in Priism can launch ewbp for you.
- ExamineData (HTML online help, text online help)
- Displays the data as a spreadsheet like table.

Priism | Applications by category | Applications by name

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- ffilter (HTML online help, text online help)
- Applies a cylindrically symmetric two or three dimensional filter.
- Filter2D (HTML online help, text online help)
- Applies one of a variety of two dimensional filters (mean, median, ...) to smooth or sharpen an image.
- Filter2D(Fourier) (HTML online help, text online help)
- Applies a 2D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.
- Filter3D (HTML online help, text online help)
- Applies one of a variety of three dimensional filters (mean, median, ...) to smooth or sharpen an image. The three dimensions can be x, y, and z or x, y and time.
- Filter3D(Fourier) (HTML online help, text online help)
- Applies a 3D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.
- Filter4D(Fourier) (HTML online help, text online help)
- Applies a 4D Butterworth, Gabor, or sum of Gaussians filter using Fourier domain techniques.
- find_axis (HTML online help, text online help)
- find_axis is an application to determine the orientation of the tilt axis for a single-axis tomographic series. The Alignment + Reconstruction user interface in Priism can launch massnorm for you.
- FindBorder (HTML online help, text online help)
- 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 (HTML online help)
- Has several more or less sophisticated methods for selecting points from a data set.
- FixBadPixel (HTML online help, text online help)
- Uses a bad pixel list generated by Resolve3D and applies it to a data set to interpolate the data values at bad pixels.
- fixtf (HTML help file, text help file)
- Applies corrections to non-radially averaged transfer functions.
- Flip (HTML online help, text online help)
- Rearranges the data to interchange one axis (x, y, z) for another.
- FPPolygons (HTML online help, text online help)
- Is similar to 2DObjFinder but can also work with data that is marked by region numbers and can associate the polygons into three dimensional volumes.
- FPwrSpec2D (HTML online help, text online help)
- 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 (HTML online help, text online help)
- 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.
- FPwrSpec4D (HTML online help, text online help)
- Calculates estimates of the 4D power spectra from the Fourier transform of the input with the option to average over multiple input blocks or smooth the final result.
- FTransform2D (HTML online help, text online help)
- Calculates a two-dimensional forward or reverse Fourier transform of the input.
- FTransform3D (HTML online help, text online help)
- Calculates a three-dimensional forward or reverse Fourier transform of the input.
- FTransform4D (HTML online help, text online help)
- Calculates a four-dimensional forward or reverse Fourier transform of the input.

Priism | Applications by category | Applications by name

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- gpurecon (HTML online help, text online help)
- gpurecon generates a 3D reconstruction from a single-axis tomographic series. It uses one or more GPU cards to accelerate the calculation. The Alignment + Reconstruction user interface in Priism can launch gpurecon for you.
- gpureproj (HTML online help, text online help)
- Is a command-line application to reproject a reconstructed volume to form a single-axis tomographic series. It uses servers outfitted with graphics cards to perform the calculations.
- header (HTML online help, text online help)
- Is a command line utility to display a Priism data file header.
- headit (HTML online help, text online help)
- Is a command line utility to edit Priism data file header.
- HisEqual (HTML online help, text online help)
- 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.
- Image Capture (HTML online help, text online help)
- Performs a series of screen captures from a Priism image window in order to generate a sequence of image files or a movie. Replaces the TiffMovie application that was part of previous versions of Priism.
- ImageArith (HTML online help, text online help)
- Is a utility for adding, subtracting, multiplying, dividing, or scaling data sets.
- ImgToMat (HTML online help, text online help)
- Converts from Priism's native format to a MATLAB workspace file (.mat).
- imod2bprm (HTML online help, text online help)
- Converts an IMod xf file and tilts file to a .bprmMn file for Priism.
- IncreaseRes (HTML online help, text online help)
- Magnifies a data set.
- Insert Tilts (HTML online help, text online help)
- Is a command-line application (insert_tilts) and an application with a graphical user interface (insert_tilts_i) to add an extended header with tilt angles to an MRC file with tomography data.

Priism | Applications by category | Applications by name

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- k2corr (HTML online help, text online help)
- k2corr detects and corrects bad pixels in raw data from Gatan's K2 camera.
- LCE 2D (HTML online help, text online help)
- 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 (HTML online help, text online help)
- Functionally similar to LCE 2D but uses a three dimensional neighborhood (either x, y, and z or x, y, and time) to calculate the local mean and contrast values that are factors in the contrast enhancement.
- Line Profile (HTML online help, text online help)
- 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.

Priism | Applications by category | Applications by name

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- massnorm (HTML online help, text online help)
- massnorm is an application to determine a consistent set of intensity scaling factors for a single-axis tomographic series. As part of that, it can estimate an offset to apply to the nominal tilt angles so that zero tilt in the corrected angles corresponds to the shortest path of the electron beam through the sample. The Alignment + Reconstruction user interface in Priism can launch massnorm for you.
- MatToImg (HTML online help, text online help)
- Converts a MATLAB workspace file (.mat) to Priism's native format.
- Measure FPS (HTML online help, text online help)
- Is a monitor function to determine the number of redraws per second as a diagnostic or performance measure.
- Merge / Reorder (HTML online help, text online help)
- Is a command line utility (mergemrc) or application with a graphical interface (mergemrc_i) to combine or reorder IVE image data files.
- Monitor (HTML online help, text online help)
- Manages an image window.
- MonToPS (HTML online help, text online help)
- Is a monitor function to generate a PostScript version of what is displayed in the image window.
- Movie (HTML online help, text online help)
- Automates the process of moving through the sections in an image window.
- Mrc2CCP4 (HTML online help, text online help)
- Converts Priism's native image format into CCP4's variant of the MRC format.
- Mrc2Image2000 (HTML online help, text online help)
- Converts Priism's native image format into the native format for the MRC Cambridge Image Processing System.
- Mrc2Spider (HTML online help, text online help)
- Converts Priism's native image format into Spider's native format.
- Mrc2tiff (HTML online help, text online help)
- Converts Priism's native format into TIFF.
- Mrc2txt (HTML online help, text online help)
- Converts Priism's native image format into text.

Priism | Applications by category | Applications by name

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- NewConvolution (HTML online help, text online help)
- Is very similar to Convolution but removes restrictions on the size of the kernel.
- Normalize (HTML online help, text online help)
- Linearly rescales each section of a data set so that each section has the same range of values.
- Percentiles (HTML online help, text online help)
- Given one or more cutoff values, c(i), find the intensity values, v(i), such that v(i) is the smallest possible intensity where the fraction of the data set with intensities less than or equal to v(i) is at least c(i).
- pf2psf (HTML help file, text help file)
- Computes slices through the point spread function (PSF) from an image of the pupil function.
- pffit (HTML help file, text help file)
- Fits Zernike polynomials to a pupil function image.
- pfimage (HTML help file, text help file)
- Computes a pupil function image from a parametric description of the pupil function.
- pfocusramp (HTML online help, text online help)
- pfocusramp can inverse filter, phase flip, or filter a single-axis tomographic series to account for the CTF of the electron microscope.
- phretavr (HTML help file, text help file)
- Retrieves an image of the pupil function from a series of z slices through the point spread funcion.
- PickPoints (HTML online help, text online help)
- Allows you to interactively select points from an image window. To convert the generated list of points into a model for 3DModel use PickToModel. Also, the points are directly usable by a number of other applications.
- PickToModel (HTML online help, text online help)
- Generates a 3D model file from the output of PickPoints.
- Point Values (HTML online help, text online help)
- Displays the data value and scaled image value corresponding to the location of the mouse pointer.
- Preferences (HTML online help, text online help)
- Displays and allows the modification of the default startup parameters for image windows.
- Preprocess2D (HTML online help, text online help)
- Can subtract the background, taper, and pad.
- Preprocess3D (HTML online help, text online help)
- Can subtract the background, taper, and pad.
- Preprocess4D (HTML online help, text online help)
- Can subtract the background, taper, and pad.
- Priism (HTML online help, text online help)
- Is a graphical interface (menu-bar) to most IVE applications.
- priism_dump_queues (HTML online help, text online help)
- Prints out the configuration of Priism's queues.

Priism | Applications by category | Applications by name

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- RA (Refine alignment) (HTML online help, text online help)
- Is a batch application to iteratively refine the alignment parameters for an EM tomographic data set.
- radialft_asym (HTML help file, text help file)
- Radially averages the 3D Fourier transform of a point source to generate an OTF for deconvolution.
- RadProj (HTML online help, text online help)
- Can perform different kinds of projections, including radial averaging, that project a data set on a Cartesian grid to a polar, spherical, or cylindrical coordinate system.
- RAGPU (Refine alignment (GPU)) (HTML online help, text online help)
- Is a batch application to iteratively refine the alignment parameters for an EM tomographic data set. It uses servers with graphics cards to perform the reconstruction and projection calculations.
- ReduceRes (HTML online help, text online help)
- Produces a reduced resolution data set by averaging over adjacent pixels.
- Region MMM (HTML online help, text online help)
- Calculates the min, max, and mean of one or more selected regions of a data set.
- RegionGrowing (HTML online help, text online help)
- Given a list of points, identifies regions about those points based on a threshold criteria.
- reproj (HTML online help, text online help)
- Is a command-line application to reproject a reconstructed volume to form a single-axis tomographic series.
- Resample2D (HTML online help, text online help)
- Generates a resampled data set by some combination of shifting the origin, rotating the axes, or changing the pixel spacing.
- Reverse (HTML online help, text online help)
- Reverses one or more of the x, y, or z axes.
- Rotate3D (HTML online help, text online help)
- 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 (HTML online help, text online help)
- Is a command line application (rotfast; rotfast_i is a graphical front-end) to generate a projection series (2D views of the data set as it is rotated about the y axis).
- RunProj (HTML online help, text online help)
- 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.

Priism | Applications by category | Applications by name

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- SaveWindow (HTML online help, text online help)
- Is a monitor function to save the data set associated with the image window to a file.
- Scale (HTML online help, text online help)
- Is a monitor function to adjust the image scaling and show the image histogram.
- SelectGrColors (HTML online help, text online help)
- Is a monitor function to select precedence for the 12 colors used to draw graphics on top of the image.
- SelectImgColors (HTML online help, text online help)
- Is a monitor function to toggle between single wavelength (pseudocolor) or multiple wavelength (RGB) display and to select the colors for multiple wavelength display.
- simplex (HTML online help)
- Is a command line application to align multiple wavelength data.
- Slider (HTML online help, text online help)
- Is a utility for simultaneously changing sections in all open image windows.
- Straight (HTML online help, text online help)
- Cuts out a tube of data about the points specified in a model file.
- superimpose_psf (HTML help file, text help file)
- 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 an OTF for deconvolution.
- SurfHarmMod (HTML online help, text online help)
- Takes a model file (one appropriate for use with 3DModel) and fits the objects in the model with spherical harmonic expansions.

Priism | Applications by category | Applications by name

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- T-RunProj (HTML online help, text online help)
- 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.
- tapir (HTML online help, text online help)
- tapir generates a 3D reconstruction from a single-axis tomographic series. It uses an iterative algorithm with positivity constraint. The Alignment + Reconstruction user interface in Priism can launch tapir for you.
- Threshold (HTML online help, text online help)
- 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.
- Tiff2mrc (HTML online help, text online help)
- Converts TIFF files into Priism's native format.
- Tracer (HTML online help, text online help)
- Can trace the axis of a tube-like structure.
- vaxmrc2mrc (HTML help file, text help file)
- Is a command line utility for converting IVE data written on a VAX.
- ViewFile (HTML online help, text online help)
- Opens an image window which is attached to a disk file.
- VolumeBuilder (HTML online help, text online help)
- Assembles two-dimensional polygons into a three-dimensional model and can report some of the typical measurements for such a model.
- VolumeViewer (HTML online help)
- Does interactive volume rendering (projects the data set to a 2D view).

Priism | Applications by category | Applications by name

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- Watershed (HTML online help, text online help)
- Implements a watershed segmentation algorithm.

Priism | Applications by category | Applications by name

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modified September 12, 2018

IVE Development Team (ive@msg.ucsf.edu)