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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.

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ActinFiberShiftAnalysis

Last changed: 2 years 43 weeks ago

This project serves to measure the dynamics of actin fibers using a bleach zone and/or bright fiducial point as points of reference. Actin fiber can be photo-marked using localized photo-bleaching. A region of interest along the actin fiber is to be used for the generation of a kymograph. The bleach zone is seen as a dark band in the kymograph, while bright fiducial point on the actin fiber is seen as a bright band. This script generates a kymograph based on Tif movie. It divides the kymograph into upper and lower part.

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ALP Alternate Line Profile

Last changed: 42 weeks 1 day 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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Automated Cell Tracker

Last changed: 5 years 38 weeks ago

This program will automatically track a user defined object (cells) through a stack of images and output the X and Y pixel coordinates of the object, as well as the distance moved and velocity for each frame of the movie. Two zip files are provided (click "View all releases" to see and download them both). The zip file "Automated Cell tracker" contains three files: Cell Tracker.pxp, CTIPN.ipf and Cell Tracker Instructions.ihf. Before you open the .pxp file, place the .ipf file under the User Procedures file folder and the .ihf file under the Igor Help Files folder.

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ColorScaleSliders

Last changed: 5 years 10 weeks ago

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.

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EccentricXPS - Analysis and Organisation of XPS Spectra

Last changed: 36 weeks 5 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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iPhys

Last changed: 20 weeks 3 days 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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iSpectra: A Toolbox for the Analysis of Spectral Images recorded on SEM-EDS systems

Last changed: 2 years 8 weeks ago

iSpectra is an open toolbox for the analysis of spectral images (SI's) recorded on scanning electron microscopes (SEM's), equipped with energy dispersive spectroscopy (EDS) systems for chemical analysis. iSpectra provides various tools for visualising chemical variability within a SI but is primarily written to create true phase maps, rather than more commonly used elemental x-ray distribution maps. iSpectra imports SI's in Lispix format and exports cumulative phase spectra in industry standard EMSA format along with graphical output.

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Kymograph analysis

Last changed: 6 years 45 weeks ago

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

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Line Scan Analysis

Last changed: 4 years 10 weeks ago

A procedure for generating kinetic profiles from analysis of intensity values from confocal line scans.
Sequential line scans are imported into 2D waves from either TIFF or Zeiss LSM* files.

Analysis options include:

  • choice of statistical test run on line scan data
  • ability to set inter-line scan-interval
  • stat values output to data table
  • creation of a graph and curve fit options

Running "Line Scan Analysis" from the Macros menu creates a panel (see screenshot).

(* requires the LSMreader.pxp written by Stephen R Ikeda

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Localizer - localization microscopy toolkit

Last changed: 5 years 19 weeks ago

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:

LSM (Zeiss) Image Reader

Last changed: 9 years 27 weeks ago

The LSMreader project is designed to open and read *.lsm files created by Zeiss LSM laser scanning confocal microscopes. Images are stored as Igor 2D or 3D (stacks) waves. Meta data are stored in strings or text waves. A subset of the meta data can be optionally stored as a wave note with each image. Individual parameters in the wave note can be extracted using the Igor functions StringByKey and NumberByKey.

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MATLAB Functions

Last changed: 7 years 15 weeks ago

The biggest barrier to Igor adoption is usually knowledge of another environment's language. One of these is MATLAB. If a MATLAB users sits down to write Igor code, sometimes they have a hard time figuring out what the equivalent function in Igor is the function they know in MATLAB. And even if they find that function, if they haven't programmed in Igor, they might get stuck on the syntax.

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IGOR.6.20.x-0.x-dev2010-Aug-05Development snapshot for Igor 6.20.x and aboveHelp

Multilevel Thresholding

Last changed: 7 years 42 weeks ago

This is a first rough try at implementing "A fast multilevel thresholding algorithm" by Liao, Chen, and Chung, which is based on a "maximized between-class variance" criterion originally due to N. Otsu (IEEE Trans System Man Cybernetics, 1979).

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Quick ROI inspector

Last changed: 23 weeks 6 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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Semi-Automated Routines for Functional Image Analysis (SARFIA)

Last changed: 13 weeks 11 hours 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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Sensicam Driver

Last changed: 5 years 27 weeks ago

Driver for accessing Sensicam CCD cameras.

The interface still has some bugs (sudden crashes, no image with long exposure > 12s). I don't have the time to fix that. Please feel free to download the sourcecode below and fix it. However, if your changes are shown to improve the code/function, please upload the improved version so everyone can use that.

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SimpLiFi - Simple line profiles for TEM/STEM images

Last changed: 31 weeks 6 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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Slideshow

Last changed: 9 years 22 weeks ago

This Igor experiment takes a folder of images and lets the user manipulate them a little bit and produce slide shows. A web page can be generated, a QuickTime movie made, or the slides can be played in Igor.

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SWC dendrite pruner

Last changed: 2 years 36 weeks ago

Code to downsample neuronal morphologies generated in SWC format, for example by the simple neurite tracer in FIJI.

Instructions
Load your SWC file as a 7 column wave
Call "Prune(SWC, spacing)"
where SWC is your neurone and spacing is your desired 3D distance between points.
Will generate a new wave called pruned and show you a projection of the two waves.

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Tracer

Last changed: 6 weeks 4 hours ago

Tracer is a utility for digitizing data from images of graphs (which could be scanned or perhaps extracted from PDF files). The image is scaled according to the plot axes, and data are created in an attempt to follow a trace across the image between endpoints marked by cursors. The data are extracted at the resolution of the image (one data point per pixel). In the event that the curve does not form a continuous path between the cursors (due to poor image resolution or use of dashed lines), the procedure attempts to search for the next line segment.

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