Imaris

3D and 4D Real-Time Interactive Data Visualization

www.bitplane.com

Visualization platform that delivers all the necessary functionality for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

Originally designed for light microscopy but the new releases are also compatible with number of electron microscopy formats:

Imaris

• dm3, Gatan Digital Micrograph• imod, mod IMOD binary files• mrc, electron density format

Available for Windows (XP, Vista, 7) and Mac OS (OS X 10.5 or later)

Imaris consists of eight unique modules that can be individually combined to perfectly match the researchers imaging needs.

Imaris• Imaris core• MeasurementPro• ImarisXT• ImarisTrack• ImarisColoc• FilamentTracer• ImarisCell• Imaris InPress

Additional modules• AutoAligner• AutoDeblur• ImarisBatch

Imaris core module

Imaris is Bitplanes core software module that delivers all the necessary functionality for visualization, segmentation and interpretation of 3D and 4D microscopy datasets.

Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size.

Conveniently load, process and visualize images acquired from almost any confocal and wide field microscope to gain new and groundbreaking insight from your image data.

Up to seven additional modules may be integrated with the core Imaris to enable specific user functionality.

Volume rendering• MIP (Maximum and Minimum Intensity Projection)• Blend Projection, weights the data that is closer to the viewer• Real-Time Shadow Rendering• Normal Shading

Minimum Intensity Projection

All visualization modes except MIP (min) require to invert the original dataset.

Surfaces• Automatic Iso-Surfaces with interactive thresholding• Automatic Local Contrast Surfaces• Automatic Region Growing• Surface Scissors• Manual Tracing

SBF-SEM dataset

Volume rendering

Surfaces• Automatic Iso-Surfaces with interactive thresholding• Automatic Local Contrast Surfaces• Automatic Region Growing• Surface Scissors• Manual Tracing

Automatic isosurface with manually defined threshold

values

Spots

• Automatic Creation of Spots• Manual Creation of Spots

Automatic creation of spots

a point-like structure that can be visualized as a sphere.

The advantage of the “Spots Object” is that local maxima can be identified in images with 10’s or 100’s of thousands of objects.

Other Features• Advanced On-Line Interaction With The Object• Kinetic Depth Effect, InMotion• Navigation Window• Filtering• Image editing• Smart Handling of Huge Images (50GB or more)• Simple in use movie editor, export to QuickTime, AVI, MPEG, or flash.• Multithreading

• Access to ImageJ/Fiji plug-in library

Imaris MeasurementProenables researchers to extract critical statistical parameters from their microscopy images thus allowing for the quantification of scientific findings.

MeasurementPro adds shape, size, and intensity based measurement capabilities to the volume rendering, surface rendering and object detection features of Imaris.

It allows researchers to interactively classify, group, and filter segmented objects based on any of the calculated statistics.

Imaris MeasurementPro• Intensity Statistics• Size Statistics• Shape Satistics• Positional Statistics

• Filtering of surfaces with statistic parameters

Selection of 4 largest objects

Imaris InPressAn image says more than a thousand words. But sometimes you want to add a few words to an image.

Imaris InPress provides the tool to place labels on structures in 3D to enhance presentations and publications effectively.

ImarisXTImarisXT acts as a two-way interface between Imaris and classic programming languages, (e.g. C++ and Matlab).

It allows rapid development and integration of custom algorithms that are specific and tailored to scientific applications where generic image processing would fail.

Imaris XT bridges the gap between complex code developed by image analysis specialists and the standardized, easy to use interface for visualization and analysis of Imaris.

+ Simple to use

+ Efficient rendering (- possible artifacts)

+ Access to ImageJ/Fiji plugins library

+ Connection to Matlab ( - if you pay)

+ Object statistics ( - if you pay)

- Costly ca. ~5000 € for each module

- Main focus to light microscopy applications

- Terrible manual segmentation

- Only one volume can be loaded at the time

- Hard to evaluate results of modelling

- Own data format that results in duplication of data

Imaris : Pros and Cons

Matlab

The Language of Technical Computing

www.mathworks.com

MatlabMATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.

• Mathematical functions for linear algebra, statistics, Fourier analysis, filtering, optimization, and numerical integration

• 2-D and 3-D graphics functions for visualizing data• Tools for building custom graphical user interfaces• Development environment for managing code, files, and data• High-level language for technical computing

MatlabBasic Matlab and more than 48 toolboxes

Available on• Windows (XP, Vista, 7) x32 and x64 bit• Mac OS X (10.6.4 and above) x64 bit• Linux (Ubuntu 10.04, 10.10; RedHat 5.x, 6.x; SUSE 11.x; Debian 5.x)

For image processing it is recommended to have:• Matlab• Image processing toolbox (free alternative is the Diplib library www.diplib.org)• Parallel processing toolbox (optional)

Matlab, segmentation of rice grains

>> I = imread('rice.png');>> imshow(I);

thresholding

>> bw = im2bw(I,112/255);>> imshow(bw);

Matlab, segmentation of rice grains

>> I = imread('rice.png');>> imshow(I);

Morphological Opening to Estimate the Background

>> background = imopen(I,strel('disk',15));>> imshow(background );Subtract the Background

Image from the Original Image

>> I = I – background;>> imshow(I);

Matlab, segmentation of rice grains

>> level = graythresh(I);>> bw = im2bw(I, level);>> imshow(I);

Threshold the Image

>> Size = regionprops(bw,'area');>> hist([Size.Area],50);

Define size of the rice grains

Microscopy Image Browserwww.biocenter.helsinki.fi/~ibelev/im_browser.html

List of Key Features:

• Powered by Matlab;• Load/Import multiple image and video formats;• Generation of 3D image stacks;• Brightness, contrast, gamma, image mode adjustments, resize, crop functions;• Actions Log;• Automatic/manual image segmentation with help of filters or manual tools (magic wand, lasso, brush...) in XY, XZ, or YZ planes;• Statistics for objects;• Optimizations for parallel processing;• Correlation/displacement analysis (for 2d datasets with time dimension);• Export of images or models to Matlab, Amira, IMOD, TIF formats;• Model visualization using Matlab isosurfaces.

Microscopy Image Browserwww.biocenter.helsinki.fi/~ibelev/im_browser.html

Microscopy Image Browserwww.biocenter.helsinki.fi/~ibelev/im_browser.html

Microscopy Image Browserwww.biocenter.helsinki.fi/~ibelev/im_browser.html

+ Huge amount of possibilities in mathematical analysis

+ Exceptionally good documentation

+ Large number of custom functions (file exchange, Diplib library)

+ Easy achievable parallel computing on CPU or GPU

- Costs ca. 500 € + 200 € (for each desired toolbox)

- It is not a program but mostly a collection of different functions

- Limited 3D rendering possibilities for large datasets

Matlab : Pros and Cons

SBF-SEM Dataset for modelling

Break

Amira

Imaris

Matlab