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NRFit

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Neutron and X-ray reflectivity analysis package:

  • Use Parratt formalism
  • Simple and easy to use
  • Provide a number of functions for roughness
  • Installation:

  • Option1: Download anywhere on your computer and open_file/procedure from 'File' menu in IgorPro.
  • Option2: Download and copy it into Igor Procedures folder in IgorPro. It will shows up in the menu.
  • Note: if it complains about FONT, select your favorite font and apply it to all experiments. And new users might want to turn ON Tips from the Graph menu.
  • Downloads:

    Chemical Bonding Curves Demo

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    ChemicalBondCurvesPackage

    Overview

    This demonstration experiment shows the shapes of curves for potential energy and force for seven expressions commonly used in chemical bonding. They include ionic, Born-Mayer, Mie, Morse, Buckingham, Lennard-Jones 6-12, and Hooke's Law. The potential is in a dimensionless form of U/Uo versus distance as r/ro, where Uo is the potential at equilibrium distance ro. Force is dimensionless by its maximum value Fmax.

    Features

    ColorScaleSliders

    Downloaded 485 times
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    Screen Shot 2011-10-03 at 12.48.52.png

    ColorScaleSliders includes a single procedure file that lets you adjust the color scaling of false-color image plots using sliders. By combining smooth adjustments with immediate feedback, this helps you optimize the appearance of false-color plots, and allows you to find fine details.

    ColorScaleSliders also includes a similar slider-driven approach to combining up to three different images into a single RGB image. A potential use could be the visualization of multicolor fluorescence data.

    Kinetic Reaction Demo

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    KineticReactionDemo.png

    Overview

    This package is a demo that was created for a class in chemical kinetics. It illustrates the behavior of a chemical reaction network A <--> I --> P under various settings of rate constants, equilibrium conditions, and temperature.

    Features

    Use the checkboxes to turn on / off equilibrium of the first reaction and running the second reaction.

    Use set variable inputs to change pre-factors, activation energies, and reaction enthalpy. Use a slider to set the equilibrium constant or reaction temperature.

    LogBook

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    logbookpanel

    Overview

    This provides a control panel to input systematic logbook information in to a notebook, including a header, a graphic (window or picture), notes, and a history reading. It also allows you to execute commands from the note field and capture the history.

    The DEVELOPMENT SNAPSHOP (below) currently contains the latest bug fixes and features

    Localizer - localization microscopy toolkit

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    Screen shot 2011-04-19 at 18.03.06.png

    NOTE: binaries for Localizer can now be downloaded from http://sushi.chem.kuleuven.be/svn/Localizer. The source code is available at https://bitbucket.org/pdedecker/localizer.

    Localizer provides a full package for performing localization and fluctuation analysis in superresolution fluorescence microscopy (PALM, STORM, SOFI, pcSOFI). The package comes in two parts, an XOP that is responsible for performing fast and efficient calculations, and an Igor procedure that provides a graphical front-end.

    The XOP includes operations for a full analysis, including:

    Synchronized Windows

    Downloaded 149 times
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    Igor supports exterior panels that stick to the target window, but only for graphs and panels.
    SyncWin extends this idea to any pair of target windows (also tables, layouts, notebooks).
    To use, create two windows and install the link between them using SyncWinInstall().
    The following examples are also given in the procedure file.

    Example 1:

    string myGraph = "MyOtherGraph"
    Display /N=$myGraph /W=(300,90,500,190)
    Display /N=MyFirstGraph /W=(350,100,550,200)
    SyncWinInstall(myGraph)

    Example 2:

    string myPanel = "Panel0", myTable = "Table0"

    Sticky Notes

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    Screenshot of Stickies in action

    Just type away while your mouse is over a graph to create a "Sticky" (a.k.a. sticky note, or text box)

    Usage:
    1. Create a graph, bring it to the front.
    2. Call InstallStickies() for the top graph window or choose "use stickies in top graph" from the Stickies menu.
    3. Point the mouse somewhere inside the graph, start typing.
    That's it.

    Full documentation in the Procedure file.

    Generic Window Hook

    Downloaded 314 times
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    Screenshot of Generic Window Hook in action.

    GenericWindowHook.ipf provides
    1) a generic window hook function that monitors events, GenericWinHook(), and
    2) an installer function, InstallGenericWinHook(), that sets up an exterior panel (dubbed here the "event panel") to show all monitored events.

    - Works for any window that can receive events (Graphs, Tables, Layouts, Panels, Notebooks).
    - You can simply use the event panel to examine what really happens to your window while developing your own hook function.
    - You can also use the GenericWinHook() code as a starting point for own your hook function.

    Usage:

    Fiber Composite Designer

    Downloaded 313 times
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    FiberCompositeDesigner

    Overview

    This is a package that was developed to show how uniform, continuous, fiber composites behave using different input parameters. You can vary the densities, modulii, strengths, and fiber volume fraction. Graphs show the stress-strain behavior of the system, the intrinsic density or fiber weight fraction, and the iso-strain or iso-stress modulus or specific modulus of the composite. Everything is self-contained.

    Visualization and Analysis of Broadband Transient Absorption Data

    Downloaded 1434 times
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    Quick visualization of data with TA Analysis Procedures - version 4

    Chirp correction procedures landed in version 4.2 and have been updated in version 4.3. Please continue to email with any comments or bugs.

    This package includes a set of functions for processing and graphing wavelength and time-resolved absorption data. This code was designed to process data created by the Helios Femtosecond Transient Absorption spectrometer produced by Ultrafast Systems, LLC. However, it will work with any data with the format:


    0, time_1, time_2, . . . , time_M
    wavelength_1, deltaOD_1_1, deltaOD_1_2, . . . , deltaOD_1_M

    PicoHarp File Access for Igor Pro

    Downloaded 747 times
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    This procedure is based on the File Access Demo in Matlab script written by Peter Kapusta, PicoQuant GmbH, September 2006.
    It was ported to IGOR Pro so that the binary data files (*.phd) created by the PicoHarp 300 time correlated single photon counting module can be directly read and analyzed.

    This procedure has been tested with version 2.0 of the PicoHarp file format (since Sept 2006) and is compatible with the most current hardware models.

    MatrixFileReader XOP

    Downloaded 471 times
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    The MatrixFileReader XOP enables Igor Pro to read data acquired with the MATRIX Data acquisition system developed by Omicron Nanotechnology GmbH. The files are not interpreted directly, rather they are accessed through libraries from the Vernissage Toolkit by the same company.

    Main Features
    • Very fast wave creation from a broad range of SPM/STS data types
    • Meta data conservation for a proper measurement documentation
    • No detour via the flat file format required
    • Check for recently acquired bricklets in the result file
    • Extensive documentation inside Igor
    • Works with data from all MATRIX versions
    • Possibility to access the raw untransformed data, therefore compatible with all matrix data types
    • The complete source code is available under a FLOSS license (LGPLv3 or later) for maximum flexibility and openness

    pFLIM - an analysis program for time-domain fluorescence lifetime imaging microscopy (FLIM) data

    Downloaded 471 times
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    We have developed a highly accurate and efficient code for the analysis of time-domain FLIM data (‘‘pFLIM’’ for precision FLIM). Our analysis code accounts for all significant instrumental artifacts (e.g., the instrument response function (IRF) and spatially inhomogeneous background events) and is rigorously based on both conventional and novel statistics. The code is described in detail in the manuscript:

    Precise measurement of protein interacting fractions with fluorescence lifetime imaging microscopy, Walther et al., Mol. BioSyst., (2011), DOI: 10.1039/c0mb00132e

    Kymograph analysis

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    Kymograph analysis

    These functions can be used to analyse 2D kymographs. This file has several dependencies, all of which are included in the project SARFIA.

    Driving and Acquiring Data from UV-Vis Spectrophotometer

    Downloaded 486 times
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    Milton-roy-UV-vis.png

    This is a very simple program to get parameters from the user for a UV-Vis absorption spectrum, and then drive the Milton-Roy Spectronic Genesys 2 UV-Vis spectrophotemeter to acquire the data and display it in real time.

    The procedure is very basic, but it works. Please let me know of any bugs or mistakes.

    The IGOR procedure file should contain adequate commenting. The procedure makes use of the VDT2 IGOR XOP (external operations). So, make sure that the appropriate XOP and help files are linked in your "IGOR Extensions" folder.

    Touchstone File Import, Analysis, & Plotting

    Downloaded 390 times
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    Project contains procedures that perform the following functions:

    - Load Touchstone files (thanks to Howard Rodstein for doing most of the footwork)
    - Convert single-ended 4 port s-params to 2 port differential s-params
    - Create group delay waves from imported s-params
    - Plot Impedance
    - Add data marker to plot with one click
    - Add a limit line to a plot to check if imported s-params meet a predefined threshold
    - Format plots to add a legend, change trace colors, add title, and add correct axis labels
    - ReadMe file included for installation and operation assistance

    Progress Window

    Downloaded 263 times
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    Creates a progress window panel(s) which supports hierarchical progress bars that are easy to activate/update/deactivate from a function. Overhead for updating the progress window is minimal.

    XOP function stub generator

    Downloaded 227 times
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    From a specially crafted C header file, this Perl script can generate all necessary (resource file, header, and function) stubs for creating a XOP.
    See the file example-header.h for an example input file, the output is in the files functionBodys.cpp, functionBodys.h, resourceFile.rc.
    Requirements: A recent version of Perl and ctags from http://ctags.sourceforge.net/.
    Call the script as ./xop-stub-generator.pl example-header.h.

    Annotation Tools

    Downloaded 265 times
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    Annotation Tools Panel

    Overview

    This provides a Control Panel as input to manipulate annotations on a graph so that they can be precisely positioned vertically and horizontally.

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