Features of BiaQIm

  The latest version is 2.5 Alpha, January 2008 

Step-by-step Guide to Deconvolution

Click here to download the 191 Kb PDF that gives you a step-by-step account of how to use BiaQIm to deconvolve an image. This is based on an extract from chapter 11 of the full User's Manual. The example uses files that are provided in the standerd BiaQIm distribution so you can work along with it.

List of Main Features

Click here to go straight to the changes since v2.41

Load and Save raw data arrays upto long double floating point precision

Load and Save standard image file formats (8 and 24bpp bmp, FITS, pgm, ppm)

Easy 'click-n-drag' loading of images and raw data arrays. Supports multiple file selection.

Interchange between different file types / data types easily.

Full real-time display of pixel co-ordinates, display values and original data values at any pixel under the mouse pointer at all times.

Reversible RGB <--> HSV colour space transformation. Can be done in real-time on-the-fly (limited only by computer speed and image size)

Whole image statistics calculations with RGB, HSV support. Standard output: size, min, max, range, quartiles, interquartile range, mean, median, variance and standard deviation. Centile calculator allows the user to calculate any centiles with variable histogram bin size.

Calculate image stats on the fly for real-time histogramming and centile-based display mapping

Image list manipulations, batch processing, batch renaming and image animation

Animate image lists with real-time value mapping, threshold viewing, LUT mappng and histogramming. The interactive histogram and line plotting routines allow real-time linkage to manual thresholding and pixel mapping and allow RGB or HSV components to be displayed simultaneously or separately. Histogram scaling can be manually selected and fixed and histogram data can easily be saved in a tsv file.

Thresholding via interactive slider bars or user-supplied values. The basis for thresholding may be: display value, orginal data value or centile-based.

Thresholding according to R,G,B or H,S,V colour models with each colour channel independently controllable. Automatic thresholding via the Kittler & Illingworth minimum error method at the click of a button. This is ideal for images with bimodal histograms. Thresholdng modes support overlap thresholds. Automated batch thresholding of a list of images is available with the ability to do binary mask post-processing on-the-fly.

BiaQIm HSV-based Thresholding in Action

Click here for full-sized image. The original 24bpp colour image is shown top left. The hue, saturation and value channels are shown top mid-left to right. The resulting mask after application of the threhsold and a 3x3 rank filter is shown bottom right. HSV thresholding selects out the DAB immunoreaction product in ths example of prostate cancer stained by the ABC immunoperoxidase method for Chromogranin A. (Counterstained with haematoxylin). The HSV model is a powerful basis for colour discrimination. Note the BiaQIm threshold options dialogue box and the independent slider and edit controls for hue, saturation and intensity upper (U) and lower (L) thresholds. (The third slider control in each set is for the pedestal values during value mapping).

All thresholding supports two thresholds (upper and lower) with many thresholding behaviour options.

Value mapping between upper and lower limits and pedestal control. R,G,B or H,S,V channels separately controllable. Mapping may be performed on display values, actual data values or be centile-based. Easy hue rotation achieved via a slider bar. Automated batch image colour / value mapping is available.

Look-Up-Table (LUT) manipulations. Generate you own LUT for custom visualisation. Standard mappings include inverse, square root, logarithmic, exponential, square and custom gamma. These may be applied to the original data and separately to any channel of a colour image (R,G,B or H,S,V).

Independent X,Y (and Z for image stacks) display scaling with 'Micro-Display' support for very high zoom factors. This zoomed mode can be freely used when tracing regions of interest (ROI), etc.

Real-time X,Y,Z line plots with variable scale factors. The data from these plots can be saved as a standard tsv file for use in spreadsheets, etc.

The BiaQIm YZ-Slicer and Plotter in Action

Click here for full-sized image.XZ slicing is also possible.The images of serial sections in the image stack shown here were registered using the Biaram automated image registration programs and manipulated in 3-D using other Biaram programs.

Real-time interactive X-Z and Y-Z slice viewing in image stacks for 3-D exploration of data.

Foreground and Background mask support. Masks can be loaded or created by interactive tracing or thresholding. Logical operations and binary operations on masks. Rank filtration. Mask object labelling and object measurements. Region-based (object) statistics calculations. Object area measurements and relative area measurements to some user-specified reference area. Set image pixels under the mask to specified constant values or values derived statistically from the original underlying pixel values.

Interactive calibrated length measurements for straight lines and curved paths. Freman, Kulper and Euclidean lengths.

Automated morphometry on binary masks. When labellng a binary mask, a Chamfer 5-7-11 distance transform and an 8-connected boundary tracking is perfomed automatically as standard. Thus when the 'Region Stats' button is clicked a host of morphometric measurements is now calculated automatically for every labelled object in the field. The measurements may be calibrated to real-world units. Measurements include area (by Pick's theorum as well as number of pixels to reduce small object area bias), perimeter, minimum and maximum diamter, binary centre of mass, shape factors (including P2A and the Danielsson shape factor, equivalent width and diamter of equivalent circle, elongatedness and eccentricity). The qrm file format saves the tracking and distance transofrm data and all data necessary to calculate the morphometric measurements. The current calibration scale factors are also saved but the morphometric measurements are independent of these such that new estimates of the morphometric measurments can be calculated using different calibration scale factors at a later date if desired.

Fourier transformation (invertible) with the abilty to perform interactive frequency domain filtering. Can read in complex arrays. Display modes: Real, Imaginary, Modulus, Argument. Power spectrum easily calculated and displayed. Both FFT and 'slow' DFT available so data arrays of any size and dimensions may be transformed - not just powers of 2.

Instant proceses to support DFT functions include matrix cyclisation and 2-D data windowing using the Bartlett, Hann or Welch windows in either normal or rounded (iso-distance) modes. Data windowing is reversible.

Interactive object counting using the 6 channel differential counter. Each channel can be given its own name label. The size and colour of counter marks is variable by the user. Real-time grand total updates so you can stop when a certain number of objects have been counted. New counter features have been added in v2.41 (see below).

The BiaQIm Differential Counter in Action

Click here for full-sized image. Note that the count marks can be given individualised name labels.

Batch file renaming facility and file list generation.

An easy Windows-based interface to complex high level image processing tools. Examples linked so far include maximum entropy deconvolution and automated image registration. Batch processing is possible e.g. the deconvolution of a series of images by the same point-spread-function (psf) or the automated alignment (registration) of a stack of images of serial sections for 3D reconstruction.

When coupled to the appropriate Biaram modules many other processes are available. These include image rotation, translation, scaling and other transforms. Single and dual iage arithmetic. List averaging. Labelled region statistics. Precision de-interlacing of video fields. 3-dimensional image stack warpings and transforms. Background and shading corrections. Image file format and data type conversions. Wavelet-based de-noising and the digital total variation filter. Fourier transforms, convolutions, edge detection, histogram equalisation, rank filter, un-sharp mask, deonvolution... Plus many more!

Works under Microsoft Windows and is FREE OF CHARGE. Commercial products for Windows PCs which do the kind of things mentioned above (though no commercial package has all the features present in Biaram / BiaQIm) cost typically in the range of £2,500 for software alone and upto around £45,000 for software + computer + camera.

Features Added in v2.40 cf. v2.31

Interactive measurements now include angles

The line and histograms plots have been further improved. Cumulative histograms can be plotted at will. The line plots include a memory option to store a line plot from a previous position or different image and to overlay the plot in memory with the current plot. This allows comparison of line plots before and after a certain image process for example. The plots now have quantitative axes. Z-plots have the option to spread the abscissa according to numerical file names for accurate plotting of unevenly sampled data such as in time decay series.

The BiaQIm Line Plots and Histogram Options in Action

 Click here for full-sized image. Note that more plot options are available than shown. Normal and cumulative histogram views are available for any mode - not just HSV - by simply ticking / un-ticking the 'Cumulative' box..

Image processes added include extended options in wavelet de-noising, improved digitial TV filtration (a bug was fixed and new features added), general convolution, rank filter (the general form of the median filter), many edge detectors, unshap masking, histogram equalisation (includes local area HE and adaptive neighbourhood HE), general Fourier transform, Wavelet transform, CCD image photometric calibration tool, PSF estimation tools and six deconvolution algorithms (maximum entropy, Van-Cittert, Lucy-Richardson, Least Squares, Weiner filter, Custom method). The automated image registration program has been improved and now has the option of Normalised Mutual Information-based matching. Also, many more programs have been added to the Biaram collection including nearest-neighbours 3D image restoration and programs for 3D image stack processing.

The standard set of display LUTs (previously distributed as separate LUT files) are now incorporated into an easy drop-down menu. The ability to load custom LUTs to this menu by loading external LUT files is still available. The LUT mapping options have been extended to include a general gamma mapping.

You may now easily convert between image data types by loading in one type and simply saving in another (no need to go through the data type conversion process). Also now have the option to save the display image as a BMP file whatever the original data type.

Manual mask / ROI tracing now includes filled ellipse and rectangle draw tools and a Fourier symmetricise mask editing option to assist manual DFT filtering.

The batch renaming tool now has to option to accept an external list file as the source of the output file names and there is an option to start renaming from a user-defined point in any numbered list.

Features Added in v2.41 cf. v2.40

Enhanced manual differential counter functions: Now you can save and load a counting session so you can take breaks when performing large count tasks or keep records. Furthermore you can now transfer your counting dots to a labelled mask to perform analysis on the marked objects (e.g. nearest neighbour analysis). The interface is also improved - you cannot accidently reset the counter as in previous versions.

Batch Renaming: The renamer can now handle arbitrary (constant) step sizes in file number - the increments do not have to be in steps of 1.

3D Slicing: Grey level scaling is now applied to XZ and YZ slices when examining an image stack.

Binary processing: You can now save the Chamfer distance transform separately as a raw doubles array.

The interface has been improved and some bugs in v2.40 have been fixed. There is now extended support for new versions of Biaram programs including Autoreg and Formula. For a detailed list of bug fixes and changes see the ReadMe.txt file that comes with the BiaQIm distribution.

Features Added in v2.5 cf. v2.41

Masking: Now you can save the components of a labelled mask invdividually: Boundary tracing and distance transform (grey lebel BMP), distance transform (raw doubles option) and labelled image (8bpp indexed colour). A bug that only accepted lower case '.bmp' extension imagesto be drag-dropped into M1 or M2 has been fixed. A bug in the 'Fourier Symmetricise' option for masks has been fixed.

Batch Renaming: Several new options are provided - you can strip full path names from the file names to make qfl files more portable; you can strip a list from obsolete files; the renamer now renames any .qih files associated with the image files (previously these were ignored). The GUI has been upgraded.

3D Slicing: LUT manipulations are now shown in the XZ and YZ slices. Support for colour image slicing has been extended to allow colour separation and LUTs to be applied to colour XZ and YZ slices. The X,Y,Z plot windows can now be effectively closed by clicking the 'x' at the top of the window.

Code upgrades: The overhauled and upgraded general Fourier transform, convolution and other processes are now included in this version

The interface has been improved and some bugs in v2.41 have been fixed. There is now extended support for new versions of Biaram programs including Autoreg v2.62, Convolution, Deconvolution (Deconvolve, DeconME, DeconLS), Fourier, Edge detection and spatial Transforms. For a detailed list of bug fixes and changes see the ReadMe.txt file that comes with the BiaQIm distribution.

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  Dr P. J. Tadrous 2000-2008