median
AMEN 1.1.7
Free and open source Annotation, Mapping, Expression and Network tools for your Mac more>> Free and open source Annotation, Mapping, Expression and Network tools for your Mac
AMEN is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as chromosomal location, annotation, interaction and expression data.
System requirements:
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Enhancements
Three bugs occured when expression data contained missing values in the following modules:
- Average/median expression calculation
- Standard deviation filtration
- Standardized normalization
- The "affy" package does not provide the "normalize.quantiles" function anymore. AMEN now uses the "normalizeBetweenArrays" function from the "Limma" package into the quantile-quantile normalization module.

ImageJ 1.43j
ImageJ can be considered to be a high-quality and handy public domain Java image processing program which is inspired by NIH Image for the Macintosh. more>>
ImageJ 1.43j can be considered to be a high-quality and handy public domain Java image processing program which is inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later virtual machine. It can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations. It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles.
It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. Image can be zoomed up to 32:1 and down to 1:32. All analysis and processing functions are available at any magnification factor. The program supports any number of windows (images) simultaneously, limited only by available memory. Spatial calibration is available to provide real world dimensional measurements in units such as millimeters. Density or gray scale calibration is also available.
Major Features:
- Runs Everywhere: ImageJ is written in Java, which allows it to run on Linux, Mac OS X and Windows, in both 32-bit and 64-bit modes.
- Open Source: ImageJ and its Java source code are freely available and in the public domain. No license is required.
- User Community: ImageJ has a large and knowledgeable worldwide user community. More than 1700 users and developers subscribe to the ImageJ mailing list.
- Macros: Automate tasks and create custom tools using macros. Generate macro code using the command recorder and debug it using the macro debugger. More than 300 macros are available on the ImageJ Web site.
- Plugins: Extend ImageJ by developing plugins using ImageJ's built in text editor and Java compiler. More than 500 plugins are available.
- Toolkit: Use ImageJ as a image processing toolkit (class library) to develop applets, servlets or applications.
- Speed: ImageJ is the world's fastest pure Java image processing program. It can filter a 2048x2048 image in 0.1 seconds (*). That's 40 million pixels per second!
- Data Types: 8-bit grayscale or indexed color, 16-bit unsigned integer, 32-bit floating-point and RGB color.
- File Formats: Open and save all supported data types as TIFF (uncompressed) or as raw data. Open and save GIF, JPEG, BMP, PNG, PGM, FITS and ASCII. Open DICOM. Open TIFFs, GIFs, JPEGs, DICOMs and raw data using a URL. Open and save many other formats using plugins.
- Image display: Tools are provided for zooming (1:32 to 32:1) and scrolling images. All analysis and processing functions work at any magnification factor.
- Selections: Create rectangular, elliptical or irregular area selections. Create line and point selections. Edit selectoins and automatically create them using the wand tool. Draw, fill, clear, filter or measure selections. Save selections and transer them to other images.
- Image Enhancement: Supports smoothing, sharpening, edge detection, median filtering and thresholding on both 8-bit grayscale and RGB color images. Interactively adjust brightness and contrast of 8, 16 and 32-bit images.
- Geometric Operations: Crop, scale, resize and rotate. Flip vertically or horizontally.
- Analysis: Measure area, mean, standard deviation, min and max of selection or entire image. Measure lengths and angles. Use real world measurement units such as millimeters. Calibrate using density standards. Generate histograms and profile plots.
- Editing: Cut, copy or paste images or selections. Paste using AND, OR, XOR or "Blend" modes. Add text, arrows, rectangles, ellipses or polygons to images.
- Color Processing: Split a 32-bit color image into RGB or HSV components. Merge 8-bit components into a color image. Convert an RGB image to 8-bit indexed color. Apply pseudo-color palettes to grayscale images.
- Stacks: Display a "stack" of related images in a single window. Process an entire stack using a single command. Open a folder of images as a stack. Save stacks as multi-image TIFF files.
Enhancements:
- Added the Image>Overlay submenu with Add Selection, Add Image, Hide Overlay, Show Overlay, From ROI Manager, To ROI Manager and Flatten commands (example1, example2).
- Added the ImageRoi class (JavaScript example).
- Bruno Vieira contributed Colony Counter, a plugin for counting bacteria colonies in agar plates.
- Marcel Austenfeld contributed Twain Scan, a plugin that uses the open source library from www.mms-computing.co.uk to capture images from Twain campatible scanners and cameras.
Requirements:
- Mac OS X 10.5 or later
functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering. It does geometric transformations such as scaling, rotation and flips. Image can be zoomedLicense:Freeware
License:Freeware
License:Freeware
Statistics and Charts 2.0
Statistics and Charts allows you to create charts from single and double statistical density data more>>
The chart types included are Bar, Control, Frequency/Group Distribution, Percentage, Line, and Pie. Also several types of Statistical output can be obtain such as mean, standard deviation, mode, range, median, medrange, and upper and lower control limits.
Keiths Image Stacker 4.2
Keiths Image Stacker - Image processing program more>>
What Keiths Image Stacker provides, more than anything else, is a workspace in which to align many similar images (say from a quicktime movie of Jupiter taken through a telescope with a webcam) and then to produce a stack of the images, which consists of a single image that comprises either the sum, or the average, or some value in between of the individually stacked images.
Stacking images is a well-established method for increasing the signal-to-noise ratio in a series of similar images. True "information" will shine through the stack, while random noise will drop out.
Enhancements:
- In the Unsharp Mask and Laplacian Sharpening Interfaces, if you attempted to redefine a the preview bounds but released the mouse button without dragging a rectangle, this could cause subsequent crashes later on. Should be fixed.
- v4.1 introduced a bug into the Open FITS file interface, in which each channel opened would erase any existing channels in the stack. This made it impossible to recover an RGB stack from three FITS files. The problem has been solved.
- The sliders in the Power Spectrum Sorting Interface were being memory leaked. Fixed.
- Fixed a bug that could cause a crash when the Clips Window is closed.
- Centroid alignment wasnt using the proper algorithm to determine a pixels overall value (using average instead of max of RGB components). Fixed.
- Preview bounds for a variety of operations were not properly displayed in the FrameStack window if the FrameStack window size did not perfectly match that actual FrameStacks size. Should be fixed.
- The Laplacian Sharpening Interface did not respect the pin-zero and pin-one boxes when creating the final result after hitting the OK button. This would cause the final result to suddenly change so as to not match the preview that was available immediately before hitting OK. This is fixed now.
- The Laplacian Sharpening Interface did not remember the value of the DC term properly after being closed. Fixed.
- Half bug, half missing feature in some cases, the Marking Clip Rect (cyan border around a clip) often was not drawn for many operations. Several occurances of this bug were fixed in v4.1. Several more are fixed here.
- Turns out I was calculating 2D power spectrums quite incorrectly. Sorting by power spectrum will hopefully improve now.
- A smattering of small changes and fixes to the precise dimensions of power-2 operations bounds rects and methods for getting pixels from GWorlds (inclusion of the right and bottom edges of pixels of a bounds rect primarily)
- In the Unsharp Masking Interface, if you moved the preview rect, the old preview rect was not restored to the original image. Fixed.
- If the RGB channels of the Frame Stack were independently aligned, the single channel views in the Histograms/Levels Interface were not drawn properly. Fixed (and eliminated now that those checkboxes are gone)
- If the FrameStack was rebuilt, the RGB alignments on the FrameStack were not reinitialized to (0, 0). Bug? Stupid feature? Either way, they are initialized now.
Changes:
- Added Debayering on the individual clips, for use with cameras that have been "RAW" modded to receive the Bayer pattern directly from the cameras CCD.
- Decreased the Event reaction time slightly. This vastly cuts the amount of CPU resources being hogged by the program without noticably affecting the programs performance.
- When sorting frames by power spectrum distribution, there is now a high frequency cutoff slider in addition to the old low frequency cutoff slider. The score of a frame will be the ratio of the sum of power between the cutoffs to the sum of total power. Initial experiments suggest that this can definitely improve the final sorted order of the frames.
- A few sorting methods have been completely removed because people continue to be confused as to how to properly sort the frames in such a way as to get satisfying results. At the same time, the sorting menu has been garnished with some textual notes that should prod people in the right direction under most circumstances.
- Significant changes to centroid alignment. Centroid alignment is considerably faster than difference alignment, especially when the misalignments are large. However, it may not produce the optimal alignment (I am unsure about this. Perhaps it is optimal after all, in which it is definitely superior to the difference method). Therefore, it is suggested to use centroid alignment (4-key) first and then clean up with a difference alignment using the 3-key. The 1-key and 2-key difference alignments, despite fixing large misalignments better than the 3-key method, are slower than the centroid method, which is why centroid followed by 3-key is recommended as the best overall approach.
- Added Cross-Correlation alignment. It is used in the same fashion as the existing four methods of alignment, three for difference and one for centroid. Simply hold down the 5 key and click on a clip or a selection of clips to use it. You must, however, use a power-of-two Operations Bound rect. Otherwise the program simply beeps. While this method usually works pretty well, it sometimes gets confused and produces a completely ridiculous alignment. Additionally, it is noticeably slower than the other alignment methods. Frankly, I think the centroid method is best for macro-alignments and the key-3 difference method is best for micro-alignments.
- Added a new operation on the FrameStack called Fourier Transform Editor. This allows you to literally paint out those parts of the Fourier transform of the stack that correspond to periodic interference patterns, such as the "herring bone" pattern that pervades many long exposure modified webcams. Aligning with a brightness threshold (which deals with the same problem in some cases) is still crucial, since it provides an optimal and sharp alignment, but if the final stack is not deep enough, it can still exhibit these kinds of interference patterns. This tool will virtually eliminate them. I would guess that it should also help in mitigating Bayer pattern effects, although I have not experimented with this yet.
- The centroid alignment wasnt using the brightness threshold before. Only the difference alignment was. Now centroid alignment uses it too, as does the new cross correlation alignment (although it may introduce unnatural edges into the image which could mess up the cross correlation alignment).
- Added a new checkbox to the Open Movie Interface that lets you specify that frames should be aligned on the fly as they are brought into the workspace. Not only does this allow you to align at the time of opening the file (which doesnt really save any time if you think about it), but it allows you to specify a bounds rect in the Open Movie Interface that only needs to fit around the object in the first frame, not the full drifted area of the object in all frames. This will save memory of course. Likewise this prevents the object from drifting outside the specified rect and being clipped by accident if you didnt make the original rect big enough in the first frame.
- Added four menu commands to the View menu for viewing the RGB channels of the FrameStack individually. Note that the 1, 2, and 3 command key menu equivalents have been reassigned in accordance with this change. These menu commands work even when the various operations dialogs are open. Note, however, that the channel appearances interact with the preview rects in some strange ways. I am still working on designing the best possible interface and interaction for all the possible combinations of settings.
- Removed the recently added channel checkboxes in the Histogram/Levels Interface. They are no longer necessary now that the much easier to use menu command replacements are available.
- Documentation updates.
- Resampling of the clips used to occur on the original opened-from-disk form of the clip. It now occurs on the modified form and makes the modified form the original form after resampling is completed. This means any operations become permanant and should be turned off prior to resampling if you dont want this, including dark frame subtraction, flat field division, normalization, median filtering, and alignment. In particular, this applies to deBayering as well, but deBayering must be done before resampling, as it will not work properly after resampling.
- Increased the maximum slider value for the Mask Intensity sliders in the Unsharp Masking and Laplacian Sharpening Interfaces.

Tables 1.0
Tables 1.0 is a full-featured tool to allow you to import data (in seemingly-table-like format) and ask questions, such as sum, median, mean, etc. about it. more>> <<less
PRICE 0.8.0
PRICE - image filtering and manipulation more>>
PRICE was born to support my research in image processing. So I have decided to work on a usable application that can open several file formats and apply high quality filters and other enhancements to the image.
Enhancements:
- the image representation is now a PRImage class which allows to access some fieds without fetching the TIFF image represetnation. This yeilds some speed up in some stages, like when fetching the original dimensions.
- the 5x5 convolution engine now works in color mode (separate RGB channels) too
- a small fix for the convolve progress panel that wasnt updating properly
- median filter has support for color filtering! (separate channel in RGB)
- implemented separable linear scaling
- implemented copy & paste
- faster FFT.
Adobe Photoshop AltiVec Plug-in 5.5
Adobe Photoshop 5.5 AltiVec Plug-in Resolves problems when using the Distort filters on RGB or Lab imagesm, resolves potential problems when using Median and Lighting Effects filters on small more>> Adobe Photoshop 5.5 AltiVec Plug-in Resolves problems when using the Distort filters on RGB or Lab imagesm, resolves potential problems when using Median and Lighting Effects filters on small selections, and improves speed of many operations.
G4 PowerPC, Adobe Photoshop 5.5 or later.
NIH Image 1.63
NIH Image is a public domain image processing and analysis program for the Macintosh more>>
Image can acquire, display, edit, enhance, analyze and animate images. It reads and writes TIFF, PICT, PICS and MacPaint files, providing compatibility with many other applications, including programs for scanning, processing, editing, publishing and analyzing images. It supports many standard image processing functions, including contrast enhancement, density profiling, smoothing, sharpening, edge detection, median filtering, and spatial convolution with user defined kernels.
Image can be used to measure area, mean, centroid, perimeter, etc. of user defined regions of interest. It also performs automated particle analysis and provides tools for measuring path lengths and angles. Spatial calibration is supported to provide real world area and length measurements. Density calibration can be done against radiation or optical density standards using user specified units. Results can be printed, exported to text files, or copied to the Clipboard.
A tool palette supports editing of color and gray scale images, including the ability to draw lines, rectangles and text. It can flip, rotate, invert and scale selections. It supports multiple windows and 8 levels of magnification. All editing, filtering, and measurement functions operate at any level of magnification and are undoable.
Image directly supports Data Translation and Scion frame grabber cards for capturing images or movie sequences using a TV camera. Acquired images can be shading corrected and frame averaged. Other frame grabbers are supported via plug-in modules.
Image can be customized in three ways: via a built-in Pascal-like macro language, via externally compiled plug-in modules and on the Pascal source code level.
Photoshop AltiVec G4 Plug-Ins Update
Photoshop AltiVec G4 Plug-Ins Update is an update for you to use Adobe Photoshop 5.5 on an Apple G4 Macintosh computer. more>>
Photoshop AltiVec G4 Plug-Ins Update is an update for you to use Adobe Photoshop 5.5 on an Apple G4 Macintosh computer.
This update fixes the following issues:
- Resolves problems using Photoshop 5.5 with Mac OS 8.6 or 9.0 on a multiprocessor system.
- Resolves problems using the Distort filters on RGB or LAB images.
- Resolves potential problems using the Median and Lighting Effects filters on small selections.
- Resolves potential problems with color conversions.
- Improves the speed of many operations.
Calculator+ 1.2b
Calculator+ is a lightweight scientific calculator for Mac OS X written in Cocoa Java more>>
A data table keeps all your data for statistical calculations such as the arithmetic mean or standard deviations.
Calculator+ supports Multiple memories with easy pop-up memory recall.
Version 1.2 Beta has simultaneous base conversion in binary, octal, decimal and hexadecimal numbers.
Enhancements:
- New Metallic Look
- Improved Performance and Jaguar compatibility
- Calculator Tape is attached to the main window
- Clear Button on the keypad now works correclty
- Standard deviation and variance for sample and population added. Deg, RAD, Grad is now modal (like most calculators)
- Preference Panel is added
- Software Version Update Panel Added
- Simultaneous base Conversion Panel is added
- A bug in the median function is fixed to sort the data before returning the median
- Double-pressing C (clear key) clears All.
- Clear All memories added to the memory menu
- The EE key has been added

KaleidaGraph 4.1.1
KaleidaGraph 4.1.1 is not attractive but powerful, sophisticated software for curve fitting and data analysis. more>>
KaleidaGraph 4.1.1 is designed as a professional and useful software for curve fitting and data analysis.
Major Features:
- Powerful Curve Fitting
- Built-in fits include: Smooth Weighted, Cubic Spline, and Interpolate curve fits, as well as Least Squares Regressions (linear, polynomial, exponential, logarithmic and power).
- Includes a library of over 100 industry-specific formulas you can customize.
- Utilize a predefined fit or enter your own equation (up to 9 parameters)
- Define up to 16 curve fits for simultanoues use on a single plot.
- Extrapolate curve fits to axis limits.
- Show fit equation, parameters, and R or R2.
- Copy the values of the curve fit or the residuals into the data window for further analysis.
- Data Entry
- Type data directly into the data window.
- Open Excel files directly.
- Import Tab, Space, and Comma delimited text files created in other applications.
- Read user specified data formats, including fixed / variable data widths and read / skip capabilitiy.
- Preview your data set while importing it.
- Windows and Macintosh data and graphs are fully interchangeable. DDE client support (Windows version).
- Plot Types
- Line, Scatter (X-Y), Double-X, Double-Y, Double-XY, High/Low, Step, Probability, X-Y Probability, Histogram, Box, Percentile, Horizontal Bar, Stack Bar, Column, Stack Column, Polar, Pie Summary Column, Double Y Bar, Double Y Column, Dot and Function (enter a formula).
- Binned data can be exported to a Histtogram, Step Plot, or Spike Plot.
- Plot Customization
- Fully customize your plot's attributes (axis limits, label frequency, ticks, grids, color, font, style, legend, plot size, etc.)
- Create customized color palettes.
- Control the number of markers displayed, marker shape (36 choices), size, and color.
- Control the ticks and axis labels on the X2 and Y2 axes by creating a link to their primary axis.
- Set the initial tick mark and specify tick intervals.
- Log or Linear axis settings.
- Partial decades allowed on any log axis.
- Option to use standard baseline instead of 1 on column plots with a log axis.
- Display rulers and grids for placing plot elements.
- Preview your plot changes without leaving the dialog.
- Add very flexible axis breaks.
- Cross axis at a specific value.
- Freely position the plot axis at any desired location.
- Display scientific and engineering plot labels in one of five formats.
- Drawing Tools
- Add Lines, Arrows, Boxes, Ovals, Arcs, Polygons, and Bezier curves to the plot.
- Choose from 11 different styles for lines and arrows.
- Copy, Duplicate, Group, Align, and Layer objects.
- Data Management
- Up to 160 open data windows (containing up to 1000 columns by 1 million rows each).
- Data Formats: Floating point, Double precision, Integer, Data, Time, and Text.
- Display date and time values in one of 18 formats.
- Perform multi-level sorts on the data.
- Make notes about your data (Posted Note).
- Update the plot automatically (or on-demand) if any changes are made in the data window.
- Independently adjustable column width and row height.
- Select font, font size, style, justification, font color and background color for individual columns.
- Add horizontal and vertical splits to compare different sections of the same data window.
- Perform key operations quickly using the Toolbar.
- Data Analysis & Manipulation
- Statistics
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- Parametric Tests: One and two way ANOVA (with repeated measures), t-test.
- Nonparametric Tests: Wilcoxon (Signed Rank, Matched Pairs, Wilcoxon-Mann-Whitney), Kruskal-Wallis, and Friedman.
- Post Hoc Tests: Tukey HSD, Bonferonni, Holm, Student-Newman-Keuls, Scheffe, Fisher's LSD and Dunnett.
- Descriptive Statistics: Min, Max, Sum, Points, Mean, Median, RMS, Std Deviation, Variance, Std Error, Skewness, and Kurtosis.
- Formula entry
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- Select from over 100 menu items to create algebraic equations for data manipulations.
- Use scripts to automate the process of importing data, manipulating data, creating plots, and exporting or printing plots.
- Macro Calculator
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- Use Conditional testing, Boolean testing, Subroutines, and Nested Loops.
- 1000 step RPN program capability.
- Special Plot Features
- User selectable error bars can be added with independent upper and lowe error types. Error values can be calculated or specified in a data column.
- Graphically mask data regions to temporarily eliminate data point. Numerical values of bars, columns, or pie slices can be placed automatically on the plot.
- Plot up to 20 dependent variables at once on a single set of axes. Combine multiple data sets on a single plot.
- Plot multiple X variables from one data set.
- Use the Extract button to display any data windows used to create the plot.
- Export / Import & Print
- Export plots as Metafile, JPG, GIF, TIFF, PICT, PNG, and BMP files. EPS also utilizing printer driver.
- Import Metafile, JPG, GIF, TIFF, PICT, BMP, and EPS files.
- Use the page layout feature to easily combine plots, text, and graphics on a single page.
- OLE Server support (Windows version).
- Save plots and layout in a single file.
- Seamless interaction with Microsoft Office including ungrouping of plots in PowerPoint.
Requirements:
- WINDOWS
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- Intel Pentium Processor
- Windows XP SP2, Vista and newer
- 256 MB RAM
- 45 MB available disk space
- MACINTOSH
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- PowerPC or Intel processor
- Mac OSX 10.3.9 and later
- 256 MB RAM
- 45 MB available disk space
Calgary Traffic WebCams 1.0
Calgary Traffic WebCams - Provides access to the roadside traffic webcams for Calgary more>> Euclid is a calculator and so much more. One of its unique features is that it preserves numbers in their natural state, rather than forcing everything into decimal form. For example, it remembers that 1/3 is 1/3, not 0.33333... Thus, (1/3) * 3 = 1, as it should (try this on most digital calculators and youre bound to get the incorrect 0.99999...
Euclid also supports matrix operations and sets.
25 March 2006
Euclid 2.0 released. Includes lots of new features, including support for sets and matrix operations. Euclid 2.0 contains 67 built-in functions!
New for 2.0:
added r1, r2, etc. variables, for history of results
added prefs dialog with precision remembered
added solver for simple linear polynomials: solve(5 * x + 4)
added nthPrime()
added digitCount()
added partition()
fixed ln()
ignore comments in scripts (lines starting with #)
script output goes to window instead of console
added support for sets
added mean(), median(), sum(), contains(), minInSet(), maxInSet()
evalInterval returns a set of the values generated
added properFactors(), primeFactors(), numFactors()
added support for matrices
added menu item for running a script
changed definition of fibonacci: fib(1) = fib(2) = 1
output of evalInterval now goes to window
sped up prime testing by 20x for small numbers (less than 2^63)
prime testing now takes advantage of dual processors
sped up random() for integers a bit<<less
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