sliceOmatic 5.0

  • Overview
  • Features
  • Speed
  • Additional Modules

Overview

sliceOmatic sliceOmatic, is an easy-to-use, powerful and affordable medical image analysis software that enhances researchers' ability to measure, segment and analyze multi-slice scanner data.

"SliceOmatic is a unique software package that makes the segmentation process easy, intuitive, and highly interactive.
I can't imagine using anything else."

B.J. Fregly, Computational Biomechanics Lab, University of Florida

sliceOmatic was developed for researchers in Body Composition. Its evolution is based on years of collaboration between the programmers and the researchers who use it.

SliceOmatic offers you the best segmentation process to date. Previously segmentation with MRI (Magnetic Resonance) modality was a highly labor intensive task. With sliceOmatic, morphological operators can effortlessly perform tissue segmentation. Furthermore, studies have proven that this technique is generating consistent results.

But don't take our word for it, download sliceOmatic from this web site and try it out for yourself! Without a license the program does have a few limitations (it will not let you save any results) but you can take it for a spin and see how easy it is to segment your data with it.

It is used by satisfied customers around the world:

"Ah, SliceOmatic is a work of art! It lets me take my less-than-perfect MRI data and make something beautiful out of it. I love the way it really lets you take a very close look at your data. The screen space is used very efficiently, the tools are kept out of the way and the data is front and center. The ability to quickly threshold and tag your data is great. It is then very easy to flip between morpho and edit mode and finish off the tagging. The 3d rendering and .stl file writing complete the package. The volume calculations are right on the money. While sliceO hasn't saved my life, it sure has helped save my job!
I recommend it to everyone who wants to tag MRI data..... "

David Maltbie, Procter & Gamble.

"We have been delighted with our Tomovision programs. The Slice-O-Matic program has far exceeded our expectations in terms of ease of use and quality of the output. We have found many more uses for this program than we ever expected. We have encouraged other research institutions to consider using Slice-O-Matic in their research. Thanks for the great product and the great service."

Judy Weltman, General Clinical Research Center, University of Virginia.

Features

The usual tools: SliceOmatic has, of course, all the usual tools that any good image analisys program should offer. These include tools to view the images in any direction in multiple windows, tools to filter the images, tools to measure distances, angles and surfaces on the images, and a lot more of the "basic" stuff.

SliceOmatic's Segmentation:

The process of identifying each tissue inside an image is known as "segmentation". And this is where sliceOmatic outshines the competition: its segmentation tools.

sliceOmatic balances powerful segmentation tools with a highly interactive interface, enabling you to completely control the segmentation process.

Different modalities or even different tissues within the same slice are best segmented with different techniques. SliceOmatic makes it easy for you to use the appropriate technique for each specific task. For example, in an MRI slice of the abdomen, you may want to use mathematical morphology to segment the sub-cutaneous fat and region-growing to segment the intra abdominal fat.


sliceOmatic is a research tool:

As a researcher, analysing the images is only a means to an end. What you really want is getting accurate anatomical volumes. SliceOmatic is designed as a research tool. In addition to helping you create the great images for these "wow" slides in your presentations, it will export the surfaces and volumes of each segmented tissue in a spread-sheet compatible file.


sliceOmatic and Biomechanics:

Maybe your area of research is biomechanics? Then you will want to use sliceOmatic to create polygonal meshs and/or countour lines from the segmented data. These can then be exported in a number of standard formats to be used either in finite element analisys or to create stereo-lithographic models.


Flexibility:

The wide range of formats that sliceOmatic supports makes it an ideal tool to both view and analyze all your images. You can see the list of supported image formats .

"I wanted to report back to you the outstanding results obtained with the new slice0matic software. The system works beautifully and the new software greatly eases analysis of MRI scans. Please extend my thanks to Yves for a job well done."

Dr. Steve Heymsfield - St Luke Roosevelt Hospital, NY.

Speed

Getting accurate values faster: In a technical publication, Dr Bonekamp and his colleagues compared sliceOmatic with 4 other image analysis packages. Not only did they found that sliceOmatic was among the easiest to use and had the best graphical user interface, but they also found that segmenting adipose and visceral fat with sliceOmatic was at least 3 time faster than with any of the other software.

Average time for measuring 10 slices (min)*
sliceOmatic NIHImage Analyze Hippofat EasyVision
32 322.5 100 120 97.5

* From: S Bonekamp, P Ghosh, S Crawford et all, Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging, Int J of Obesity, 32: pp.104, 2008

"[...] We consider sliceOmatic a very good choice for segmentation of abdominal adipose tissue on MR images. [...]"

S Bonekamp, P Ghosh, S Crawford et all, Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging, Int J of Obesity, 32:100-111, 2008

Additional Modules

SliceOmatic new structure is designed to allow easy integration with new modules. Anybody using the free SDK provided in the download pages can add modules to the program.

A number of these new modules can be download from our website pages. Some of these are presented further down. For a more exhaustive list, please consult the online manual.

If you want to add a module to the program, just let us know and we will provide you with any help you may require.
Some of the Additional Modules available:
  • Tool: Automation
  • Tool: DICOM_Compare
  • Tool: Pixel Interpolation
  • Tool: Scout Lines
  • Class: Border
  • Class: Clone
  • Class: Gradient Amplification
  • Class: RR2D
  • Class: RR3D
  • Mode: Histogram
  • Mode: MR Spectroscopy

Tool: Automation

DICOM_compare This tool enable you to automate some actions.  It can be used to read files and perform scripts for each files, or perform scripts for each frames, or simply perform scripts a number of times.  For example it can be used to take one snapshot of each frames, or to create an animation of a 3D object rotating, or in an industrial setting, automate the analysis of images acquire from a continuous process.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Tool: DICOM_Compare

DICOM_compare This tool integrate the standalone tool DICOM_Compare from TomoVision inside sliceOmatic. It enable you to see the DICOM tags associated with any of the loaded frames. You can either compare these tags with the DICOM definition for the same modality or with the tags of another frame. This is very useful if you want to use the Mixer, Multiplex or DICOM Tree classes.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Tool: Pixel Interpolation

interpolation interpolation
This module was developed by TomoVision for Yajima Nobuhiko of the Image Labo in Japan.

This tool enable you to "smooth" the images at higher magnifications.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Tool: Scout Lines

scout_lines This module was developed by TomoVision for the BrainBody group at the University of Toronto, Canada.

This tool enable you to display a line representing the position of a frame in all the other frames that that frame crosses. It will also enable you to visualize in real-time the current position of the cursor in all the other frames. And finally you can select the current frame by pointing at it in the scout image.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Class: Border

Mixer class This class will enable you to add borders around the frames.

This can be useful if part of the information you want to segment is outside the field of view. Adding a border enable you to extrapolate outside the frame.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Class: Clone

clone class This module was developed by TomoVision for Yajima Nobuhiko of the Image Labo in Japan.

This class will create 2 branches in the database tree. One branch contain the original images, the other an exact clone of these images. Different treatment can be applied on the GLI images of each branch, but the segmentation TAG images will be identical in both the original and the cloned branches.

This class can be useful to compare the results of other classes that modify the GLI images (such as "Filter" or "Gradient"). For example, if you create a tree with the classes: Root / Clone / Filter / Frame, you can then apply different filters to the original and clone branches and compare the results. With that tree, the shortcut key "Insert" / "Delete" will toggle between the original and cloned images.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Class: Gradient Amplification

Gradient class This module was developed by TomoVision for the LIO group of the ETS in Montreal, Canada.

This class enable you to artificially increase the gradient around a specific target GLI value. This will help segmentation techniques that are gradient based (such as "Morpho" and "Snake"). It can be used for example in segmenting CT images where you know you want to segment at specific Hounsfield values but do not want to use threshold based techniques. By increasing the gradient at the desired Hounsfield value, you insure that the gradient based technique will find the correct boundary.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Class: RR2D (Rigid Registration 2D)

rr2d rr2d This class will enable you to register slices in 2D (in the plane of the slices).  It can be used, for example, to re-align series if you need to move a patient between acquisitions.  This is a landmark based registration technique.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Class: RR3D (Rigid Registration 3D)

rr3d rr3d This class will enable you to register series in 3D using rigid transformations (translation, rotation and scaling).  This is a landmark based registration technique.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Mode Histogram Segmentation

Mode Histo This module was developed by TomoVision for Jeffrey Cooley of McMurdoch University in Australia.

This mode is used to segment the images with the help of the histogram.

For more information, please consult the sliceOmatic 5.0 Online User's Manual

Mode Histo

Mode MR Spectroscopy

Spectroscopy This module was developed by TomoVision for Robert Ross of Queens University in Kingston, Canada.

This mode enable you to analyse MR spectroscopy data.

Note:
At this time sliceO only recognise Siemens datasets. If you have any other kind of datasets, please contact us! We need sample data...

For more information, please consult the sliceOmatic 5.0 Online User's Manual


Image Gallery
Scroll
to Top