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Packages include individual Igor procedure files or collections of Igor procedure files that are related, as well as external operations (XOPs). To browse ALL projects (including those that have not been officially released) click on the Advanced Browse link above.

July 18, 2017

Gene set enrichment analysis report handling for graphing in Cytoscape

Last changed: 4 weeks 3 days ago

This project handles gene set enrichment analysis (GSEA) output from the Broad Institute resource (http://software.broadinstitute.org/gsea/index.jsp) comparing enrichments between two groups and providing output to be graphed in Cytoscape (http://www.cytoscape.org/).

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July 4, 2017

MatrixFileReader XOP

Last changed: 6 weeks 3 days ago

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
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July 2, 2017

miniAna

Last changed: 6 weeks 5 days ago

miniAna

An Igor Pro procedure with offers an analytical environment for miniature events, written to analyze miniature EPSCs recorded in in vitro brain slice preparation of mice. Several parameters are obtained on each event (timestamps, amplitude, decay time, interevent interval etc) and the parameters can be exported as a comma-separated value file. Averaged trace of recorded events can also be prepared as a graph.

Getting Started

Prerequisites

* tUtility (https://github.com/yuichi-takeuchi/tUtility)

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June 30, 2017

iPhys

Last changed: 7 weeks 7 hours ago

iPhys is a dual image analysis / electrophysiology acquisition and analysis suite. Readable formats include TIFF image files, text data files and iPhys generated data files. The software was developed with increased automation of basic procedures in mind. For example, the user doesn't need to specify a file name for saving acquisition files, as they are automatically saved into the working directory. The user enjoys an extensive graphical interface with sticky windows (making dragging multiple windows easy), easy to activate and close plots and one click generated complex analysis modules.

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June 14, 2017

tClamp16

Last changed: 9 weeks 2 days ago

tClamp16

Igor Pro GUI which offers a data acquisition environment with InstruTECH ITC16.

Getting Started

Prerequisites

* Igor Pro 6.1 or later
* InstruTECH ITC-16 and a host interface
* ITC legacy XOP (ITC_X86_V##.XOP, ITC_X86_V## Help.ihf)

Installing

Similar to that of tClamp18 (https://github.com/yuichi-takeuchi/tClamp18).

Work flow

Similar to that of tClamp18 (https://github.com/yuichi-takeuchi/tClamp18).

Help

* Click "Help" in tClamp16 menu.

Versioning

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tClamp18

Last changed: 9 weeks 2 days ago

tClamp18

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June 12, 2017

bpc_ReadAbf

Last changed: 9 weeks 4 days ago

bpc_ReadAbf is an Igor Pro extension (XOP) that allows one to import pClamp ABF 1.x and 2.x binary files into Igor Pro.
bpc_ReadAbf is compatible with Igor Pro 32bit running on Windows 32bit or 64bit, it requires Igor Pro 5 or later.

Molecular Devices Corp, the company selling pClamp, provides a file support package (FSP) to aid software development. This FSP
is available for 32bit Windows only. I created a very simple XOP that basically wraps some of the functions provided by the FSP.

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June 10, 2017

tNeuroshare

Last changed: 9 weeks 6 days ago

tNeuroshare

Igor Pro GUI for importing any neurophysiology data in neuroshare format.

Getting Started

Prerequisites

* Neuroshare.XOP (http://www.nips.ac.jp/huinfo/documents/neuroshare/index.html)
* Neuroshare-compliant DLL (http://neuroshare.sourceforge.net/DLLLinks.shtml)
* tUtility (https://github.com/yuichi-takeuchi/tUtility)
* SetWindowExt.XOP (http://fermi.uchicago.edu/freeware/LoomisWood/SetWindowExt.shtml)

This code has been tested in Igor Pro version 6.3.7.2. for Windows and supposed to work in Igor Pro 6.1 or later.

Installing

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tSort

Last changed: 9 weeks 6 days ago

tSort

An Igor Pro GUI which offers a spike sorting environment for extracellular recordings with microelectrodes.

Getting Started

Prerequisites

* tUtility (https://github.com/yuichi-takeuchi/tUtility)
* SetWindowExt.XOP (http://fermi.uchicago.edu/freeware/LoomisWood/SetWindowExt.shtml)

This code has been tested in Igor Pro version 6.3.7.2. for Windows and supposed to work in Igor Pro 6.1 or later.

Installing

1. Install Igor Pro 6.1 or later.

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June 6, 2017

tUtility

Last changed: 10 weeks 3 days ago

tUtility

This procedure (tUtility) offers a GUI (control panel) for general purpose analyses with necessory library.
It is written for analyses and figure preparation of in vitro patch-clamp data.
But it can be utilized for other analyses including in vivo intra- and extracellular recordings, calcium imagings etc.

Getting Started

Prerequisites

* PPT.XOP (http://www.mpibpc.mpg.de/groups/neher/index.php?page=software)
* SetWindowExt.XOP (http://fermi.uchicago.edu/freeware/LoomisWood/SetWindowExt.shtml)

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Quick ROI inspector

Last changed: 10 weeks 3 days ago

//// This marquee tool is for analysing time series movies.
////Use the marquee tool to mark an ROI, right click and select quickroi.
////This is then appended to the image with its coordinates printed to the history.
////The average of the pixel values within the ROI in each frame is calculated and
//// shown in the wave QROI. If you select a new ROI this everything is updated.
/// You can also use the "subtract background" button to subtract the average of the
////ROI pixels from the whole image on a frame by frmae basis. Useful for analysing Ca imaging movies

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May 30, 2017

CMAPAnalysis

Last changed: 11 weeks 3 days ago

CMAPAnalysis

An Igor Pro procedure with GUI used for averaging, analyses, figure preparation of evoked potentials. The parameters for analysis are latency, duration, amplitude, rectified area, and conduction velocity of the averaged evoked potentials. These parameters are stored on a table and can be exported as a csv file.

Getting Started

Prerequisites

* IGOR Pro 6 (https://www.wavemetrics.com/)

This code has been tested in Igor Pro version 6.3.7.2. for Windows and supposed to work in Igor Pro 6.1 or later.

Installing

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May 24, 2017

Semi-Automated Routines for Functional Image Analysis (SARFIA)

Last changed: 12 weeks 2 days ago

SARFIA has been developed for the analysis of functional fluorescence data, for instance recordings from cells labeled with fluorescent calcium indicators. However, it allows access to a variety of inbuilt and custom-written image processing functions.

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May 23, 2017

FitXPS

Last changed: 12 weeks 2 days ago

FitXPS is a procedure to fit a core-level X-ray photoemission spectrum (XPS) to a Voight profile with Shirley or Tougaard type background.

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May 22, 2017

bpc_Dialogs

Last changed: 12 weeks 3 days ago

The bpc_Dialogs XOP provides some external functions that facilitate writing interactive Igor procedures/functions. While similar functionality could also be achieved to some extend with Igor code, bpc_Dialogs.xop is supposed to make life a little easier, both for the programmer and also for the user. bpc_Dialogs.xop supports 32bit Igor running on 32bit or 64bit windows. It was developed and tested with Igor 6.2. But it uses standard Windows programming techniques, and there is a good chance that the XOP works just fine also with Igor 7.

bpc_Dialogs adds the following functions to Igor:

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May 9, 2017

Arc Hull Baseline

Last changed: 14 weeks 3 days ago

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.

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April 11, 2017

SimpLiFi - Simple line profiles for TEM/STEM images

Last changed: 18 weeks 3 days ago

The SimpLiFi package provides an interface for extracting and analyzing line profiles from TEM/STEM images. This tool is in part a simplified version of the Image Line Profile tool provided in the ImageProcessing package by WaveMetrics ( SimpLiFi does not handle paths - only straight lines - and only greyscale images). It is also in part modified to mimic functionalities of the Line Profile tool available in Gatan's Digital Micrograph:

- A Frame is displayed on the image to show the width over which the profile is drawn

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April 7, 2017

XOP function stub generator

Last changed: 19 weeks 9 hours ago

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, functions.cpp, functions.h, functions.rc.
Requirements: A recent version of Perl and utags from https://ctags.io.
Call the script as ./xop-stub-generator.pl example-header.h.

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March 23, 2017

Unit Testing Framework

Last changed: 21 weeks 20 hours ago

This project aims at providing a complete set of tools for programmers for writing and maintaining unit tests.

Features:
  • Runs on Windows and MacOSX
  • Completely documented and with lots of examples
  • Includes more than ten test assertions coming in three versions
  • Allows for the arbitrary grouping of test cases
  • Easily expandable and adaptable
  • Support for executing test suites from the command line
Planned features (open for collaboration):
  • Threadsafe test assertions
  • Igor Pro help file documentation
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March 8, 2017

EccentricXPS - Analysis and Organisation of XPS Spectra

Last changed: 23 weeks 2 days ago

EccentricXPS is an Igor Pro procedure initially written to load, display and analyze the two-dimensional x-ray photoelectron spectroscopy (XPS) images produced by our VG Scienta SES 200 hemispherical analyzer at the University of Erlangen-Nuremberg. EccentricXPS can load and display the images from the raw .txt files produced by the SES software (version 1.2.2, build 37) and then convert the images to normal one-dimensional spectra, which can be easily displayed, compared and fitted, either as single spectra or in bulk.

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March 6, 2017

A tool that can autocomplete commands typing

Last changed: 23 weeks 3 days ago

Autocompletion is very common in a real programming language IDE, such as VS, but it is a pity that IGOR Pro does not support this. Therefore, I have written a tool to do autocomplete in IGOR Pro.
The Package includes two files: Autocomplete_JXW.ipf, datacache.dat, the first is the procedure file, the second is a database file, contains function/operation name and a brief description of it.

How to use:

1 open Autocomplete_JXW.ipf and compile it,

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GenCurvefit

Last changed: 23 weeks 3 days ago

GenCurvefit uses differential evolution (genetic optimisation), with a user defined fit function, to fit data with up to 50 independent variables. The technique is extremely good at finding global minima in Chi^2, even with poor starting guesses.

Copyright - Andrew Nelson and the Australian Nuclear Science and Technology Organisation 2007.

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IGOR.5.04.x-1.4.x-dev2014-Sep-21Development snapshot for Igor 5.04.x and aboveHelp
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March 1, 2017

XMLutils - XOP to facilitate working with XML files

Last changed: 24 weeks 1 day ago

An external XOP designed to facilitate working with XML files. Based on the libxml2 library by Daniel Veillard, released through the MIT licence for libxml2

Win32 and Mac Universal binaries are available

XMLopenfile - open an XML file
XMLsavefile - save a modified XML file
XMLclosefile - close (and save?) an XML file
XMLelemlist - List all ELEMENT_NODES in XML document
XMLdocDump - Dump the entire XML file to IGOR history
XMLlistXPath - get the nodes that match a specific XPath
XMLstrfmXPath - get content from nodeset selected by an XPath and return it as a string

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IGOR.5.04.x-1.x-dev2012-Jun-19Development snapshot for Igor 5.04.x and aboveHelp
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February 17, 2017

Point Labels

Last changed: 26 weeks 55 min ago

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.

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February 8, 2017

Visualization and Analysis of Broadband Transient Absorption Data

Last changed: 27 weeks 2 days ago

Updated to work with current Helios (v14) and EOS software. 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

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February 2, 2017

Periodic Table Selector

Last changed: 28 weeks 1 day ago

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.

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January 31, 2017

Fermi Distribution + DoS Plot

Last changed: 28 weeks 3 days ago

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.

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January 29, 2017

ALP Alternate Line Profile

Last changed: 28 weeks 5 days ago

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.

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January 16, 2017

Baseline Spline Fit

Last changed: 30 weeks 4 days ago

For fitting and subtracting spline type baselines to spectroscopic data. A spline is a continuous curve that passes through points ("nodes") selected by the user. This Igor procedure file provides an interface that allows the user to position the points and see the resulting baseline. Some sub-menus are added to the macro menu, including an option to subtract the baseline from the data.

Usage

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December 31, 2016

CommandPanel

Last changed: 32 weeks 6 days ago

igor-CommandPanel

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

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