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EccentricXPS - A Tool for Fitting XPS Spectra

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An Igor procedure for XPS analysis. The procedure was written to load and analyse XPS spectra acquired in our lab, but will work with all waves present in Igor.

Point Labels

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Puts labels on waves at position of cursor A.
Labels are the x position of the point.
Uses wave scaling or an x-axis wave.
Multiple labels on each wave.
Multiple waves in one graph.
Labels can be deleted on a per-wave basis.

Periodic Table Selector

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Periodic table with mutiple elements selected

Periodic Table Selector (PTS)

What and Why:
J. J. Weimer has contributed the very nice Periodic Table Menu package. It shows data for one element at a time, but I needed a way to quickly select several elements. PTS is derived from Periodic Table Menu and has the following characteristics:

- Graphically select any number of elements, the resulting list is processed separately.
- Use mouse clicks or very fast mouseover to select or deselect elements.
- Panel can be rescaled (as in Periodic Table Menu).
- Panel can be closed, then later reopened, the selection is retained.

Fermi Distribution + DoS Plot

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FD DoS Picture.png

This demo shows the curves for the Fermi-Dirac distribution function multiplied wiht a projected density of states (DoS) from a free-electron metal. Change parameters with sliders to see the changes in the curves.

ALP Alternate Line Profile

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ALP main window and profile region on

Why ALP?
The Igor 7 image line profile has fewer features than in Igor 6. Wavemetrics is not currently planning to make significant changes, the
workaround suggested is to use IP6 procedures. Some issues are:
- The profile graph cannnot be modified, or the data explored, for example with a cursor.
- Does not take wave scaling into account.
- No longer possible to graph a profile, it can only be saved. (Has been changed in Igor 7.02)
- The saved wave is now a triplet. This is not visible in the default New Graph menu, inexperienced users can not easily graph it themselves.

IR Shifted-peak fitting

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This is a set of routines designed to fit temperature-dependent amide I infrared spectra of proteins and peptides. It has been shown that these peaks are temperature-dependent. The data is fit to a sum of Gaussian peaks, with center position and width of each peak assumed to shift linearly with temperature. In addition, the model allows an equilibrium between peaks, so that each peak may (optionally) increase or decrease in amplitude with temperature. The change in amplitude with temperature is modeled as a two-state equilibrium.

CommandPanel

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CommandPanel

igor-CommandPanel

CommandPanel.ipf provides an alternative command-line interface for Igor Pro.

Graphical Memory Display

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For long term projects, it's easy for an experiment file to get very large and accumulate a lot of waves that might not be needed. This is a command line function that provides an interactive graphical view of the waves in the indicated parent folder and all immediate subfolders. All of the waves in each subfolder are color coded by their size.

Top panel buttons:
Update: updates the display if waves have been deleted or added
Folder Size: appends a graph of the size of each folder (in terms of cumulative # rows in all the waves)
Remove: removes folder size graph

Arc Hull Baseline

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Arc Hull is a baseline approximation for spectral data.

A concave-upward arc is defined by a circle centered at the midpoint of the spectrum. The depth of the arc is adjustable. The arc is added to the spectrum, and the lower portion of a convex hull is calculated for the resultant spectrum. The baseline consists of the sum of the arc and the convex hull.

Setting arc depth to zero creates a convex hull (a.k.a. 'rubber band') type baseline.

TEA_MT - Intensity versus time trace of fluorescent spots extraction and analysis software

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GUI of TEA_MT updated

The software was written so that all of the daily single-molecule (and other fluorescent spots) data analysis tasks are accessible at one place:
1. fluorescent spot detection,
2. co-localization of the fluorescent spots from 2 channels,
3. intensity versus time traces extraction for selected type of fluorescent spots,
4. filtering of traces
5. normalization of traces to an excitation field
6. intensity change point detection in the traces,
7. characterization of detected states,
8. manual selection of extracted traces,
9. 2D histogram plotting of the analysis results.

GIS shapefile and GeoTIFF file load

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Load shapefiles and GeoTIFF files into Igor. If the datum of loaded data is eastings and northings or false eastings and false northings, convert it to decimal lat/lon. This works for GeoTIFF images also.

There is also a macro to write shapefiles.

This experiment requires that the IgorGIS.xop is installed. (Available from Wavemetrics)

PHI SPE File Loader

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Background

This package contains a loader for PHI SPE files. The files are generated by PHI XPS and AES instruments. The procedure is based on generous and greatly appreciated contributions from the folks at this link: http://www.igorexchange.com/node/5692

Use

Here are some insights to the use of this procedure.

  • LoadPHISPEFile() - This command will load a PHI SPE file.

Color Wheel based on Color Star by Johannes Itten

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Color Wheel example 2

Utility to easily select and manipulate colors based on the color star. Color selection is interactive and can be easily applied to generate color tables. Color tables can be customized to accurately present multiple palettes

bpc_ReadAxg

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bpc_ReadAxg.png

bpc_ReadAxg is an Igor Pro extension (XOP) that allows one to import Axograph binary files (including Axograph X) into Igor Pro.
Axograph is a popular data acquisition and analysis software, especially on the Mac platform.
bpc_ReadAxg borrows from the public domain AxographIO sample code kindly provided by Dr. J. Clements, the developer of Axograph.
bpc_ReadAxg is compatible with Igor Pro 32bit running on Windows 32bit or 64bit, it requires Igor Pro 5 or later.

If you want to try out bpc_ReadAxg, please copy 'bpc_ReadAbf.xop' to your 'Igor Extensions' folder.

Apply Hex Code Color Theme to Graph

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This procedure applies an external generated or defined RGB color theme in HEX to traces in graphs. First, it converts a user-inputed textwave of HEX color codes to Igor Pro color codes, and then apply them to traces in selected graph. Two menu items will be added to "Graph" menu as "Input Color Theme" and "Apply Color Theme", so user need to selected the graph to apply the theme first to show the menu

Dynafit Simulation automation

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Use Igor to run and import simulated data from Dynafit.
Particularly useful if you want to generate progress curve in Dynafit based on enzymatic reactions and use IGOR to fit the data.

Scripts reads the Dyanfit scripts and allows you change values of the Dynafit script constants on the fly, simulate it and import the data.
The simulated data can be fit and individual observed rates are extracted and plotted onto a new graph*.

*Works for exponential and linear fit!

Edit:
Let me know if you are planning to use it for publications or would like to see any improvements?

Semiconductor Conductivity Demonstration

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Semiconductor Demo Image

This package demonstrates the behavior of conductivity for a doped semiconductor. Graphs of ln versus inverse temperature and conductivity versus temperature are shown. Sliders allow the user to change the gap energy, dopant energy, mobility ratio, and dopant amount. The curves update dynamically, and reports of exhaustion and equivalence temperatures are made.

Instructions and the theory are provided as notebooks to the demonstration.

Coding Conventions

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Coding conventions and best practices for Igor Pro development.

Completely unofficial and authored by me.

MultiGroups_stats_panel

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igor_multi_stat_panel.png

Provide a panel to perform the following 2 groups and multiple groups statistical analysis:

Mean +/- sem, normality test, variance test, cohen's D effect size
*Two groups: (paired) t-test, K-S Test, Wilcoxon Rank Test
*Three groups: ANOVA, Dunnette, Tukey

To select multiple waves hold Ctrl key when click wavenames

bpc_ReadHeka

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screenshot.png

bpc_ReadHeka is an Igor Pro extension (XOP) that allows one to import HEKA Pulse and Patchmaster data files into Igor Pro.
It is compatible with Igor Pro 32bit running on Windows 32bit or 64bit, it requires Igor Pro 5 or later.
bpc_ReadHeka is based on the work of Francisco Mendez & Frank Würriehausen the creators of the PPT software package.
It is a heavily modified and stripped down version of PPT with all functionality that is not directly related to data file loading removed.

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