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SWC dendrite pruner

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Pruned.png

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.

iPhys

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Iphys

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.

Fuzzy Lines

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Regular plot appearance

Adds the ability to generate fuzzy (blurred) lines to graphs. Parameters (width, color, line style) are controlled by Fuzzy Line panel from the Graph menu. Individual traces can be selected by right clicking the trace and selecting Fuzzy line. Currently only similar parameters for all traces on a plot is supported. Fuzzy lines are updated when traces change, but only when Fuzzy Line panel is visible.

ActinFiberShiftAnalysis

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Interface and result of the script generates

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.

FitXPS

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Example for Bi 4f XPS curve fitting with FitXPS

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

van der Waals Isotherm Plots

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vdW Isotherm Plot Package

This package provides a way to show the pressure - molar volume isotherms for a range of gases that follow the van der Waals gas law. It was created as part of assignment for a course on thermodynamics, specifically dealing with mechanical equations of state for real gases.

iSpectra: A Toolbox for the Analysis of Spectral Images recorded on SEM-EDS systems

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Screen Shot 2014-11-18 at 13.43.43 .png

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.

Chebyshev - interpolation and fitting using Chebyshev polynomials

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Chebyshev performs interpolation and fitting using Chebyshev polynomials

HSL/HCL Colour Table Creator with GUI

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ColourTab_Full.png

This package allows the user to easily create their own custom colour tables for use in other Igor plots (either to define colours in image plots, or for colouring traces/data-points).

The interface allows the user to create four distinct types of colour table:

  • Single Hue table
  • Bi-polar (Double Hue) table
  • Multi Hue Category table
  • Hue Blend table

Data Folder Size Calculator

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Data Folder Size Calculator Graph

This routine calculates the number of bytes in a selected data folder, including any subfolders. It builds on the recursive listing functions written by Jamie Boyd. The output is printed to the history window in a human-readable format. The calculation considers only numeric waves, not text waves and not strings or variables.

Scroll Wheel Zoom

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Zoom in/out of graph with scroll wheel (both x and y simultaneously), centered around mouse cursor.

Tries to zoom only relevant axes; should do ok with single plot graphs or graphs with plots in single row or column. Might not do so well if there are multiple columns and rows (a matrix of plots).

- Activate on each graph or automatically enable on all _new_ graphs.
- Activate/automatically-enable in Graph:Packages:Scroll Zoom menu or in Graph Marquee popup menu (is there a way to append to the Graph popup menu?).

Reconstruction of the spatio-temporal receptive fields of visual neurons with filtered back projection

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Retinal ganglion cell receptive field

This project provides procedures to reconstruct both the spatio and temporal receptive fields of visual neurons that have been stimulated with a series of flashed bars.

A complete description of this method along with examples of its implementation has been published in a scientific paper in J Physiol (2014) doi:10.1113/jphysiol.2014.276642 (http://www.ncbi.nlm.nih.gov/pubmed/25172952).
Please cite this paper when publishing data using this method.

Cube Helix Designer for Image Color Index Waves

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Cube Helix Design Panel

Igor implementation of "Dave Green's `cubehelix' colour scheme" described here:

http://www.mrao.cam.ac.uk/~dag/CUBEHELIX/

Quote:

This colour scheme is described in more detail in:

Green, D. A., 2011, `A colour scheme for the display of astronomical intensity images', Bulletin of the Astronomical Society of India, 39, 289.
(http://adsabs.harvard.edu/abs/2011BASI...39..289G at ADS/)

This implementation has a panel where you can design a "cube helix" color index wave and apply it to any open image plot.

bpc_ReadAbf

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import_abf.png

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.

General Import Tool

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This is a general project for importing data files from various instruments/software.
XPS:
- SpecsLab 2 (*.xml; *.xy)
- Kratos Vision 2 (*.dset)
- Spectra
- Bessy EMP TGM7
AFM:
- Gwyddion (*.gwy)
- Omicron SCALA
- Veeco HDF v3.2
- Nanotec WSxM
....

https://github.com/Yohko/importtool

nurbs

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CURBS-HMC-Gradient

MovieMaker

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MovieMaker screenshot

A small procedure that allows you to make movies out of a set of 2D waves.

How to use:

1- Drag drop the procedure file onto igor and compile
2- Run "Load Panel" from the MovieMaker menu
3- Click on Test Waves to make some test waves to play with
4- Click on Preview. Make adjustments, add annotations etc. add extra commands (if any) in command boxes to run on frames.
5- Run through frames using the slider
6- Click on "Make" to export the video

Visual Odometry

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carpet with coin

Dense VO and Feature Detection VO used for carpet and indoor

IgorCL

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IgorCL is an external operation for Igor Pro that allows you to perform calculations on your computer's CPU or GPU using OpenCL. OpenCL is a software framework that provides a uniform way to perform computation on heterogeneous devices. The authoritative source on OpenCL is the official website, http://www.khronos.org/opencl/, and particularly the OpenCL specification.

Syntax Highlighting in VIM

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Screenshot of gvim under linux

Based on the work of Peter Li, http://www.hcs.harvard.edu/~pli/code/#vim, I completely revised the syntax highlighting for Igor Pro procedures in Vim.

Install into a folder read by gvim and add the following code to vimrc

" add filetype detection for Igor Pro procedure files
au BufNewFile,BufRead *.ipf set filetype=igorpro
" Honour user settings for colors or use the default igor pro colors
" let igorpro_default_colors = 1
" If you want to use folding, activate it with
" set foldmethod=syntax

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