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CalcPad

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A notepad that functions as a calculator.

Type an expression and hit enter. Use up and down arrows to insert previously executed lines. Use shift-up/down to replace selection with previous answers. Execution environment is current data folder.

Molar Mass Calculator

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Molar Mass Calculator

A notebook that functions as a molar mass calculator. Type a formula and hit enter. The calculated mass is output to the notebook window and inserted in the clipboard.

Alternatively, from the command line: print molWt("H2O") where H2O is replaced by the formula of interest. Please use correctly capitalized element symbols!

Transfer graphs between different experiment files

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Transfer graphs completely (both data and graph it self) from one expriment to another, some like as the Save Graph package but far more convenient. One does not need to save the graph copy as a text file and not need to load it using the Load Igor Text menu item.

How to use:
1 Drag the TransferGraph.ipf to the current experiment file and compile it. A menu named "TransferGraph" is created with two menuitems: "SaveGraph" and "LoadGraph". Do the same thing to the target experiment file you want to transfer graphs to.

Loomis-Wood Add-In

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The Loomis-Wood Add-In is a package for Igor Pro that allows the creation of interactive Loomis-Wood plots for the analysis of high resolution molecular spectra.

OpenCL SGEMM implemented using AMD GPU

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This is a simple implementation of OpenCL SGEMM using AMD GPU based on various web materials, written only for 64-bit Igor Pro 7, other version not tested.

*It works only for matrices which are divisible by 16 for now.
It is not well optimized, but might serve as a starting point for users who would like to explore computing using GPU with Igor Pro.
With AMD HD 7950, it provides around a factor of 3 speed up over Intel Core i7-4790.

Encircle

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encircle.png

Encircle a cloud of data on a plot and shade the bounded region.

How to use:

  • Right click on a data point to invoke the trace menu and select "Encircle points" to draw a polygon that surrounds all of the data in the wave.
  • If you change the aspect ratio of the plot area you can repeat this procedure to update the shape of the polygon that surrounds the data.
  • Selecting "Remove Encircled Region" deletes the shaded region.

Polygons are drawn in the user back layer using axis coordinates and can be edited with the drawing tools.

Gene set enrichment analysis report handling for graphing in Cytoscape

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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/).

tClamp16

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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

tClamp18

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tClamp18

tNeuroshare

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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

tSort

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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.

miniAna

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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)

tUtility

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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)

Quick ROI inspector

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//// 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

CMAPAnalysis

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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

bpc_Dialogs

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bpc_Dialogs.png

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:

SimpLiFi - Simple line profiles for TEM/STEM images

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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

A tool that can autocomplete commands typing

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Autocomplete.jpg

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,

EccentricXPS - Analysis and Organisation of XPS Spectra

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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.

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.

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