Dave Mitchell's DigitalMicrograph™ Scripting Website

Scripts Listed By Function

Select Scripts:

Acquisition

DigiScan Presets: DigiScan capture tool, which provides a range of preset frame sizes, exposures, linesynch and signal selection options.

Image Integration: Acquires multiple images from a CCD camera an integrates them to increase the effective bit depth and signal/noise ratio.

Report Acquisition Times: Report the acquisition times for a series of open images.

Calibration

Add Adjustable Scale Bar: Adds a scale bar to the front-most image.

CCD Electron Calibrator: Applies previously determined intensity scaling values to images, to calibrate them in electrons or electrons per unit area. It requires that the conversion efficiency of the CCD be either known or measured.

Propagate Calibration: Takes the calibration of the front-most image and propagates it to all open images.

Recalibrate SADP: A simple dialog-based script which will recalibrate the front-most diffraction pattern in a range of different units.

Recalibrator: Recalibrates a folder of images which have incorrect calibrations.

Remove or Restore Calibration: Removes a calibration from an image temporarily. This can subsequently be restored.

Scale Bar Control: Allows the size, colour and font of the foremost image's scale bar to be changed and propagated to all other open images.

STEM Calibrator: Calibrates scanned images such as non-Gatan STEM or SEM, where a single calibration factor (as a function of magnification) is needed.

Transfer Calibration: Transfers calibration between images.

Diffraction

CHT Diffraction Analysis: Performs automated measurement of diffraction patterns from polycrystalline materials.

DiffTools : A suite of tools for measuring and processing selected area electron diffraction patterns.

Distortion-free Diffraction: Method to null microscope column distortion by using the objective stigmators to produce distortion-free diffraction patterns.

EF Analysis: Uses an ellipse fitting method to analyse selected area electron diffraction patterns from polycrystalline materials. Identifies and corrects any elliptical distortion which may be present.

Point and Measure: A rough and ready tool to quickly measure diffraction patterns.

RDFTools: Suite of tools for determining short range order in diffraction data from amorphous materials.

SADP Background Removal: Removes the background of a 2D diffraction pattern by thresholding or modelling.

Display

Add and Position ROI: Adds and positions a region of interest to the foremost image.

Adjust Gamma: Dynamically adjusts the gamma of the front-most image.

Apply CLUT: Applies a custom colour lookup table to the foremost image and a floating scale which shows the range of colours present.

Cascade All Open Images: Cascades all open images from top left to bottom right.

Close All Hidden Images: Closes all hidden images.

Close All Open Images: Closes all open images.

Create Image from ROI: Creates a new image from a region of interest on the foremost image.

Create or Modify Fixed ROI:Creates or modifies a region of interest on the foremost image with defined size and position.

Display Tools: A suite of tools for manipulating the way images are displayed on the screen.

Hide All Open Images: Hides all the currently open images.

Rebin by n: Rebins an image by an integer value between 2 and 8.

Reframe and Resize all Open Images : Adjusts the frame and content size of all open images, to maximise their view.

Show All Hidden Images: Displays all images which are currently hidden.

Stack Creator and Player : Converts a series of 2D images into 3D stack and allows stacks to be played as a movie.

Zoom To Full Screen: Zooms the image to fit the full size of the screen.

Zoom to ROI: Zooms the region defined by a region of interest (ROI) to fill the current bounds of the image window. Click on the maximise button (top right of the image window) to restore.

EELS/EFTEM/EDS/CL

Assign ROI as EELS Background: Uses an ROI on an EELS spectrum to fit an exponential background which can be adjusted dynamically.

Average Energy Loss: Computes the average energy loss from the front-most EELS spectrum (zero loss).

Beam Heating Calculator: Estimates the likely temperature rise in the foil due to electron beam irradiation.

CL Spectrum Imaging: Captures a z stack of images acquired at various wavelengths of the CL Spectrometer.

Compute High Frequency Dielectric Constant : Computes the high frequency dielectric constant from Epsilon 2 data.

Create Spectrum from Image: Converts a CCD image of an EELS spectrum into a conventional EELS spectrum.

Double Atan EELS Background: Fits a double atan function under EELS white lines to model the continuum, enabling the white line intensities to be determined.

EELS Dispersion Calculator: Calculates the appropriate EELS spectrometer dispersion and drift tube (or Offset) voltage for a target set of EELS conditions.

EELS Display Component Spectra: Extracts and displays each slice in a composite EELS spectrum as stand-alone spectra.

EELS Spectral Difference Minimiser: Scales and shifts the front slice of a spectrum containing two overlaid spectra, to minimise the difference between them and display the difference.

EELS Spike Remover: Removes x-ray spikes from EELS spectra.

EELSTools: A suite of scripts designed for acquiring, processing and analysing EELS spectra.

EFTEM Resolution Calculator: Computes the theoretical resolution of EFTEM images as a function of objective semi-angle, on the basis of the followiing microscope parameters: accelerating voltage, Cc, slit width and energy loss.

Gaussian Fit: Fits a gaussian to a peak identified by a region of interest. Can be used to measure full width half maxima in EELS spectra.

HADES: A script-based implementation of Dual EELS which also permits dispersion calibration and measurement of non-uniformity in dispersion and HT stability.

Import MSA EELS Spectrum from EELSdb Database: Imports spectra downloaded from the EELSdb Database as .msa files into DigitalMicrograph

Local Neighbourhood Density Threshold and Dilation: Processes x-ray dot maps to eliminate background dots (low density of dots) but retain dots in regions which contain the element of interest (high density of dots) and if necessary - fill in this area by dilation.

Map Explorer: An interactive tool for extracting intensity profiles from suites of x-ray, EFTEM maps etc.

Mean Free Path Estimator: Computes the mean free path using the mean atomic number or average density.

Savitzky-Golay Spectral Filter: A computationally efficient filter for smoothing spectra while retaining peak shape.

Scatter Plot: Computes a scatter plot from the two selected images (usually x-ray or EFTEM maps). Scatter plots show clustering where there is compositional correlation between the two maps.

Set EELS Experimental Conditions: Saves EELS experimental conditions (alpha and beta) to the local computer and allows them to be applied to spectra or spectral images.

SITools: A suite of software tools to process Spectrum Images.

Spectrum Peak Remover: Script to manually remove an artefact peak from a spectrum/profile and replace it with an interpolated (straight line) fit to the adjacent background.

Super-X Monitor: A plugin designed to monitor EDS detector performance. Designed with the FEI Super-X detector in mind, but will work with any TEM-based SiLi/SDD system.

Trace Back:Enables interactive interrogation of a scatter plot image to show regions in the source maps where composition correlation occurs.

Warp EELS Momentum-Energy maps: Warps an EELS Momentum-Energy map to remove the distorting effects of GIF aberrations about a horizontal centreline.

Select Scripts:

File Conversion

Batch Export Spectra as Tabbed Text : Exports all currently displayed profiles as tabbed text files.

Batch File Converter: Batch converts folders of files from one format to another.

Batch Import Noran CSV Files: A batch importation utility to read in text files saved in CSV format (comma separated values), from Noran System 7 EDS software.

Create a 1D Plot from a Single Column Text File: Reads in data points from a single column (carriage return delimited) text file and creates a 1D plot. The option to calibrate the plot is given.

CSV Importer: Imports x-ray, phase and PCA maps from Noran System Seven and colours them.Some other file formats are also supported.

EMSA File to Tabbed Text: Converts EMSA formatted files, such as those generated by the Noran System 6 EDS sofware, to tabbed text. Thereafter they can be replotted in any graphing package or imported into Excel for further processing.

Export Image as Tabbed Text: Exports the front-most image to a text window as tabbed text. The data is in three tabbed columns: X, Y and Value. This is then saved as a text file, for subsequent import into Excel or other plotting/analysis packages.

Export Profile As Tabbed Text: Exports the front-most profile (intensity profile, EELS spectrum etc) to a window as tabbed text. This is then saved as a tabbed text file, for subsequent import into Excel or other plotting/analysis packages.

Flip and Save: Flips all currently open images about the selected axis and then saves them to the chosen directory.

Import JEOL EMSA into Spectrum: Imports the data from a JEOL EDS EMSA spectrum file into a spectrum.

Import Noran EMSA into Spectrum: Imports EDS spectrum files (in their native EMSA format) from Noran System 7 into a spectrum.

Multiple Saves As Hi-Res TIFF: Saves all the currently open images to the selected directory as 8 bit TIFF images at full resolution.

Prepare for Printing: Places the foremost image on a page and adds footer information based on the microscope info. A good way of printing a single image.

Save all as .dm3 with a common name and counter : Saves all open images in Gatan .dm3 format, with a common name and counter.

Save All As Gatan: Saves all the currently open images in Gatan (.dm3) format, with the option to append an incrementing number at the end of the file name.

SI Dismantler: Dismantles a spectrum image into its component spectra.

Image Processing

Align Images : Script to align two images using either cross correlation or manual alignment.

Atom Colouriser: Fits a lattice of circles to an experimental high resolution HAADF image whichcan then be colourised to highlight defects etc.

Automatic Image Montaging: Joins together a sequence of overlapping images to create a montage.

Calculate Range Map and Nearest Neighbour Histogram: Script to compute the range between nearest neighbours in dot map images. A histogram of the nearest neighbour distances is also produced.

Calculate Areal Percentages in Binary Images: Sums the image to compute the areal percentages of black and white pixels in a binary image.

Canny Edge Filter: An interactive edge finding filter based on the Canny Edge Detector method.

Cross Correlate ROI with Image: Takes an image area defined by a region of interest (ROI) and cross correlates it with the whole image.

Damped Edge Filter for FFT: Filter to eliminate vertical and horizontal edge artefacts from FFTs.

Digital Dodging: Applies an intensity wedge to flatten uneven brightness in an image, such as that arising from thickness variations.

Distortion Correction: Measures and corrects distortion in images of periodic structures.

Edge Direction Colour Map: Applies a Sobel edge finding filter then thresholds the edges and colour codes them according to their direction.

Equaliser: Equalise the intensity difference across two halves of an image caused by CCD readout calibration errors.

FFT Band-Pass Filter: Provides a dialog-based interface for setting up an annular band-pass filter. This is useful for rapidly processing multiple images using a FFT mask.

FFT Filter: Script to apply a gaussian blur or Butterworth high pass or low pass filter to the front-most image. This is done using FFT methods.

Flip Image: Flips the front-most image about either its horizontal or vertical axis, into a new image.

Folder Rebinner: Rebins folders of images.

Frei and Chen: Carries out Frei and Chen image filtering for edge detection.

Gaussian Blur: Applies a Gaussian blur to the front-most image.

High Pass Filter: An image processing filter which retains only the high frequency components in an image.

HRTEM Filter: Applies a Wiener or Average Background Subtraction filter to remove contributions from amorphous phases to HRTEM images.

Hurst Texture Filter: Measures the fractal dimension of an image to convert regions with different textures into different greyscales.

Image Deshearer : Applies a linear shear to an image to remove the effects of drift.

Image Montaging: Creates an aligned montage from previously acquired images or raw (unaligned) montages.

Image Normaliser: Levels out low frequency variations in brightness in the image, such as those due to thickness gradients in the specimen.

Interactive Thresholding: Dynamically threshold the foremost image via an ROI imposed on a histogram. The resulting binary image and contour map are calculated.

Invert Image Contrast: Inverts the contrast of the front-most image. In binary valued images 0 become 1 and vice versa. In greyscale image the minimum becomes the maximum and vice versa, with everything in between scaled appropriately.

Masked Area Scaling: Script to scale the intensity of subareas of an image. These can be defined by oval/box annotations or rectangular/freehand ROIs.

Median Filter: Applies a median filter to the front-most image or a region of interest therein.

Monte Carlo 2D Gaussian Fitting: Fits a 2D Gaussian to a blob feature - such as diffraction spot or atomic column - to locate its centroid with sub-pixel accuracy.

Prewitt Filter: An edge-finding filter.

Remove FEG Fluctuations: Reduces the horizontal banding found in images acquired on cold FEG systems, where the emission undergoes sudden changes.

RL STEM Filter: Carries out a Richardson-Lucy probe shape deconvolution to sharpen atomic resolution STEM images.

Scale Image to 0-255: Scales the intensity values of the front-most image to the range 0 - 255.

7x7 Mexican Hat. Laplacian of gaussian edge detection filter which is not too sensitive to noise.

Shift SADP Centre to Image Centre: Shifts the SADP centre to the geometric centre of the image.

Simplified Phase Contrast Imaging: A script to compute the phase image from either one or a pair of images a differing defocus.

Sobel Filter: Function-based script to calculate the Sobel magnitude (or phase) of the passed in image. The Sobel filter is useful for finding edges (and their directions).

STEM Decaffeinator: Removes the flags and skips (STEM scan instabilities) from high resolution images.

Streak-free FFT : Applies a Butterworth filter prior to computing the FFT or Reduced FFT, to remove streaks in an FFT caused by the image edges.

zFocus: Extracts the optimum regions of focus to create an in-focus 2D image from a 3D through-focus stack.

Measurement

Atomic Displacement: Analyses cube axis HAADF images of ferroelectric materials to measure the displacement of atomic columns due to ferroelectric polarisation.

Cryo Fluence Measurement: Reports an average electron flux for an image, on the basis of the CCD conversion efficiency.

Compute 2D CTF Map: Computes a 2D contrast transfer function map.

Diffractogram Analyser: Analyses the front-most FFT (Thon ring pattern of an amorphous film) to determine the Cs and Defocus values.

ERF Resolution: Automatically measures resolution test images to obtain a resolution value for SEM, STEM etc.

Grating Tools: A suite of scripts with which to automate measurement of images (SEM or Optical) of diffraction gratings or other regular periodic structures.

Grid Creator: A dialog-based script which allows the user to apply a grid to the foremost image. The grid can be used to aid manual counting of features, and the pixel values at the grid line intersects are reported with some stats, for automated random measurement.

High Precision Line Length Measurement: Reports the length of the selected line to four decimal place precision.

Measure Angles: Measures the angle defined by three successive mouse positions on an image.

Measure Features: Measure average feature dimensions such as film thicknesses, by drawing multiple lines across the regions of interest.

Probe Analyser: Analyses all open CCD images of converged probes - STEM, CBD etc and reports dimensions (FWHM, FWTM), intensities, current and displays intensity profiles.

SMART: A suite of tools to measure resolution and astigmatism in scanning microscope images.

THF Peak Locator: Uses a top hat filer to locate maxima and/or minima in the foremost spectrum or intensity profile. This dialog-based script allows the top hat filter parameters to be tailored. Peak positions can be output to the Results window or saved a tabbed text.

Select Scripts:

Microscope/GIF

Acquire Rotate and Crop: Acquires an image from a CCD camera, then rotates the image and crops it to eliminate the black space introduced by rotation.

Capture Filter Control Settings: Takes a snapshot of the current Gatan Filter Control settings and saves them as an image for future restoration (see Restore Filter Control Settings).

Capture Live Profile to Stack: Captures a live profile image and saves it to a stack.

CCD Temperature Graph: Sources the dark counts from a CCD camera and plots the effective CCD temperature, and change in temperature on a graph.

CCD Temperature Monitor: Monitors the temperature of a CCD camera either indirectly from the dark counts produced by the camera (universally applicable) or from temperature information sourced directly from the camera controller (only supported on newer controllers).

Change JEOL TEM Control Screen:Provides toolbar buttons to select various pages on the JEOL in-built control screen and raise and lower the fluorescent screen.

Current Converter: Enables screen current density (read off the fluorescent screen) to be converted into a true current.

Drift Measurement: Script which periodically captures CCD images and uses cross correlation to measure the specimen drift. A cross correlation image, a vector plot (showing the direction and magnitude of the drift) and a plot of the instantaneous drift rate is displayed.

Drift Tube Scanning: Scans the GIF drift tube voltage to and fro as a background thread.

Enter JEOL Commands: Allows JEOL commands to be entered into DigitalMicrograph, to control the TEM remotely.

Faux Camera Library: Provides a library of camera manager commands to enable offline development of camera-based scripts.

Faux CL Library : A library of faux CL (cathodoluminescence) functions to enable offline script development for CL-based scripts.

Faux DigiScan Library: A library of DigiScan commands to enable script development of DigiScan-based scripts without working at a microscope system.

Faux Hardware Settings: A dialog-based script which can be used to monitor and edit the settings which are used by the Faux hardware libraries eg Faux Camera.

Faux Imaging Filter Library: Provides a library of imaging filter commands to enable offline development of GIF-based scripts.

Faux Microscope Library: A library of faux microscope control functions to enable offline script development for microscope-based scripts.

File Name Creator: Creates file names for images and spectra using user-defined terms and microscope information to expedite the saving of data.

Frame Grabber: Captures continuously the front-most live image (TEM, STEM etc) into a 3D Stack or to disk.

Hollow Cone Scanning: Creates a scanning hollow cone by tilting the beam azimuthally. As this is a software implementation, it is much slower than hardware systems. However, since dark field exposure times of many seconds are typical, the beam may complete several circuits (with judicious choice of parameters) during an acquisition. The scan runs as a background thread and so it can be set running and then images captured using normal camera acquisitions.

HT Control Panel: Provides a control panel for controlling the HT on older JEOL microscopes which use serial communication interfaces.'Read the warnings accompanying this script'.

JEOL Alpha Wobbler: Script to wobble the alpha (X) tilt on the goniometer of JEOL microscopes to allow setting of the eucentric height and to identify the tilt axis for tomography.

JEOL Free Lens Control and Degauss: Enables free lens control and degaussing of older (serial communication) JEOL TEMs, such as the 2010.

JEOL HAADF Camera Length: Script to set a short STEM camera length for HAADF on older JEOL (serial communication) TEMs such as the 2000, 3000, 2010, 3010 etc (without FasTEM).

JEOL TEM Control: Creates a palette to control the microscope from within DigitalMicrograph. This script enables the user to control the fluorescent screen, spot size, focus, brightness mag, image shift and stage shift (only useful at low mag). Designed for older JEOL TEMs with serial control.

Live Image Simulator: Script to create a continuously updating/changing image using a background thread.

Live Image Simulator - Periodic Thread: Dialog-based script which uses a periodic thread to simulate a live camera view image.

Match GIF Rotation to TEM: Rotates an image caputred on a GIF to match what is seen on the fluorescent screen.

Objective Astigmatism Helper: Fits an ROI to a live Camera View image (if the image is not 2^n x 2^n - where n is an integer). It then creates a live reduced FFT fitted with a series of yellow concentric circles, to aid correction of objective astigmatism.

Osiris STEM Probe Selector: Allows a dataset of 110 STEM probes to be searched on the basis of either target probe characteristics or microscope settings (Gun Lens, Spot Size and C2 Aperture) from which they are derived. This dataset is unique to the FEI Osiris (X-FEG source, analytical polepiece, 200kV).

Restore Filter Control Settings: Script to restore the Gatan Image Filter Control settings stored in an IFC Record (image). Use the saved records to quickly restore particular set ups during EELS sessions. This script uses files saved from the script 'Capture Filter Control Settings'.

Restore JEOL Microscope Configuration: Restores a JEOL microscope alignment from a file saved with 'Save JEOL Microscope Configuration'. 'Read the warnings accompanying this script'.

Save JEOL Microscope Configuration: Saves a custom JEOL microscope lens/deflector/stigmator configuration.

Stage Through Focus Acquisition: Acquires a 3D Stack of through-focus images on an SEM equipped with DigiScan, by stepping the stage. Read the warnings accompanying this script.

SEM Stage Scanning : Drives an SEM (or TEM) stage in an X-Y raster while capturing scanning images using DigiScan to build up a large area montage.

STEM Averager: Captures time-lapse STEM images using slow acquisition and fast acquisition stacks using continuous acquisition.

STEM Diffraction: Captures and analyses diffraction patterns at each point in a 2D STEM scan.

TEM Control: Creates a control panel to control the microscope from within DigitalMicrograph. This script enables the user to control the image shift, stage shift (X, Y, Z, A, B,) focus, magnification, spot size and brightness.

TEMDiff Acquisition: Provides a CCD acquisition control panel with two sets of acquisition conditions.

TEM Recorder: A script to acquire a sequence of images from a Gatan CCD automatically.

Through-Focus Acquisition: Scripts to enable the acquisition of through-focus image series in TEM or STEM mode.

2010F Control Palette: Creates a control panel to control both the microscope and GIF from within DigitalMicrograph.

Tilt Angle Calculator: Calculates the net tilt angle between two sets of goniometer tilts.

Tilt Scanning: Drives the beam tilts of a microscope to enable hollow cone, raster, arc and rocking scanning - as well as manual control.

Upload Lenses to JEOL TEM: Uploads a custom lens configuration, from a file saved using the script 'Save JEOL Microscope Configuration'.

Miscellaneous

Contrast Transfer Function: Computes the contrast transfer function from the supplied microscope parameters.

Countdown Timer: A simple countdown timer to keep track of time-dependent processes at the microscope.

Create a Timestamp: Creates a unique timestamp string.

DM Calculator: A simple desktop calculator for DigitalMicrograph.

Probe Broadening : From the specimen and probe properties, the STEM probe broadening due to scattering is calculated.

Relativistic Wavelength Calculator: Calculates the relativisitc wavelength of electrons from the accelerating voltage.

Struers Hardness Pattern Creator: Creates an xml file of the type used in Struers Durascan hardness systems for defining a pattern (grid) of test points for automated hardness testing.

Tag Group

Copy All Tags Between Images: Copies all the tag information from one image to another. Useful for copying calibrations, microscope info etc from a captured image (which has the tag info by default) to a calculated image which does not.

Copy All Tags to Multiple Images: Copies all the tags from a user selected image to all other currently displayed images.

Display Operator and Specimen: Script to source the current operator and specimen values from the Global Info and display them in the Results window.

Multiple Modify Operator and Specimen: Allows the Microscope Info tag data - operator and specimen - to be modified on all currently open images.

Report Image Magnifications: Reports the TEM and STEM magnifications used to acquire a folder of images.

Set Operator and Specimen: Allows the operator and specimen details to be set. These variables are stored in the Global Info settings and become appended to all subsequent acquired images.

Taggroup Transporter: Saves a selected taggroup as a settings file for subsequent upload or migration to another instance of DigitalMicrograph.

3D/Movies

Stack Alignment:Creates, splits, sums and aligns 3D stacks, such as a spectrum images.

Stack Slicer: Excises a smaller stack from a larger stack.

Utilities

Create a Synthetic HAADF Image: Synthesises a HAADF image which resembles a perovskite structure viewed down the [001] axis.

Enter User and Specimen: Creates a pop-up dialog prompting the user to select the user name from a pre-defined list of names (or add a custom name) and identify the specimen. This is added to the microscope info tags.

Generate File Number: Script to generate a file number using a reverse date format NYYMMDD00 - where N is a microscope designation, YY=year, MM=month, DD=day, 00=00 - subsequent images are incremented 01, 02 etc.

Image Downsampler: Downsamples the frontmost image to create a smaller version. Use this for creating source images for use with the 'Thumbnail Creator' script (creates hard coded image files).

Package Creator: Provides a GUI for installing and updating packages of scripts.

Protecting Scripts : Function to read the Gatan license information. This might be used to protect a script or package of scripts.

Script Cleaner: Script to remove empty white lines from a saved script file.

Thumbnail Creator: Dumps the pixel values of the foremost image into the Results window in a format whereby the hard coded data can be used in an image definition within a script.

Select Scripts: