Definiens Tissue Studio FAQ
Q: Which stains does Definiens Tissue Studio support?
A: IHC (all brown and red chromogenes), IF, and H&E.
Q: What is Definiens Composer Technology?
A: Definiens Composer Technology is a revolutionary way to easily teach the system how to recognize regions of interest (ROIs). The pathologist simply brushes on ROIs across representative images with the “paintbrush tool” and then clicks the “learn” button to complete the training process. This enables complex image analysis solutions to be created quickly, and simply without the need for programming experience.
Q: What does Definiens Tissue Studio offer for nucleus morphology?
A: Morphological features can be extracted for all nuclei on the tissue of interest. For a list of available features, please have a look into the data sheet or on tissuestudio.com. Additionally, Definiens Tissue Studio offers a module called “Nucleus Morphology and Filter”. This module can be used to extract nuclei of interest based on their morphological characteristics. The user simply brushes over the nuclei of interest and the system learns the characteristics to discriminate these from other nucleus types.
Q: Can I analyze my angiogenesis samples with Definiens Tissue Studio?
A: Yes, since version 3.0, Definiens Tissue has a built-in module for the detection of stained vessels, e.g. for CD31 or CD34 markers. It works for bright field as well as fluorescence images.
Q: I have cells that I want excluded from the analysis. How does Definiens Tissue Studio handle this?
A: Definiens Tissue Studio provides a “Cell Exclusion” feature that allows you exclude cells based on defined thresholds. For example, cells that are a certain length or width can be excluded from the analysis.
Q: What kind of immunofluorescence capabilities does Definiens Tissue Studio have?
A: Definiens Tissue Studio supports different levels of colocalization and coexpression analysis, on a nucleus-by-nucleus, cell-by-cell or simply marker area basis. The Definiens Composer Technology can be used for region of interest detection.
Q: Which image formats/slide scanners does Definiens Tissue Studio support?
A: Definiens Tissue Studio works with all standard virtual slide formats – Hamamatsu, Zeiss, Aperio, Applied Imaging, TissueGnostics, Bacus etc. – as well as generic formats like .tiff and .jpeg. Have a look at the datasheet to learn if your scanner is included.
Q: Which tissue types does the product work on?
A: Definiens Tissue Studio is intended to work on all solid tissues.
Q: What kind of results do I get?
A: Definiens Tissue Studio provides over 35 standard, and user defined results such as staining intensity (low, medium, high); area; length; roundness, compactness, shape index; as well as statistical features including: mean, min, max, std dev, etc. Additionally, Definiens Tissue Studio allows for completely new features to be created by the user; creating virtually unlimited quantification related to biomarker expression and / or tissue morphology.
Q: What is the format of the results?
A: .CSV
Q: How robust is the analysis over a typical slide set with variation in tissue preparation, staining etc.?
A: If the training is performed on 4-12 representative images of your image set, Definiens Tissue Studio will provide robust and consistent results.
Q: Does Tissue Studio only analyze images on the local workstation, or can I send batch processing jobs to my server grid?
A: You can send batch processing jobs to a server grid providing that the proper Definiens server software is installed.
Q: How long does it take to create an image analysis solution?
A: 10-20 minutes, depending on user experience.
Q: How fast is the analysis of a tissue slide given:
60,000 x 40,000 pixel slide image at 10x
50% Tissue coverage
20% of Tissue is ROI
Nuclear detection
4 engine configuration
A: The speed of the analysis would be about 10 minutes using 4 engines (CPUs). However, additional engines drastically improve analysis time.
Q: Can I develop a custom rule set plug-in for Definiens Tissue Studio in Developer XD?
A: Yes. An SDK for development of an ROI Detection algorithm for bright field images is available. For other plug-ins, the Definiens Professional Services team can help you.
Q: Can I run Definiens Tissue Studio remotely from another PC?
A: Not at this time. However, remote desktop connections can be established to accomplish this functionality.
Q: Do you integrate with third party image and data management systems?
A: Yes. Definiens takes an agnostic view of image and data management, and encourages synergy in this area. Definiens Tissue Studio is currently integrated with Aperio Spectrum and Leica Slidepath.
Q: How much does Definiens Tissue Studio cost?
A: This varies depending on the configuration. Please contact your dedicated account manager for details.
Q: Can we get an evaluation copy?
A: Please contact your account manager.
Q: How many organizations are using Tissue Studio?
A: Since its introduction in September of ’09, more than 200 licenses of Definiens Tissue Studio have been sold (status: September 2011).
Q: How often do you have functional updates to the software?
A: Typically, two times per year.
Q: Where do I find the system requirements?
A: Please have a look at the data sheet (download from the Tissue Studio website) or contact your account manager for a copy of the installation guide.
Q: How does your product compare to other digital pathology image analysis software?
A:
Simpler to use:
Using Definiens Composer Technology, Definiens has provided an intuitive, simple way to interact with images in order to facilitate the transfer of the pathologist’s knowledge into the computer, without the need for additional modules or other software. A new user can set up an image analysis solution in as little as 20 minutes.
More, Better Data:
In addition to classifications such as high, medium, and low staining intensity; cell counts; percent stain, etc. Definiens provides individual cellular morphological measurements such as circularity; elliptical fit; area; length; width; distance to tumor border; and much more. Additionally, Definiens provides true sub-cellular biomarker detection and colocalization within user-defined regions of interest; extracting and quantifying biomarker expression from nuclear, cytoplasmic, and membrane compartments. You can measure as little, or as much as you like within your tissue samples.
Faster Results:
Quick setup time, as well as rapid analysis via more efficient algorithms and utilization of client/server architecture correlates with the highest performing digital pathology image analysis solution available.
Fully Scalable:
Image analysis solutions derived using Definiens Tissue Studio can be deployed onto a server grid for rapid turnaround time of large scale projects. Need even faster results? Just add server capacity. Definiens is a proven leader in the deployment of image analysis in enterprise environments with software installed on thousands of servers worldwide.
Single Point Access:
Because Definiens Tissue Studio reads native images from most commercially available scanners, Definiens provides a single point of access for your digital pathology image analysis. You no longer have to learn multiple image analysis programs. All you need is Definiens Tissue Studio to standardize your image analysis needs.
Underlying Technology:
Definiens has been specializing in image analysis of complex images since the company’s inception in 1995 by Dr. Gerd Binning, the 1986 Nobel laureate for Physics, and inventor of Definiens’ Cognition Network Technology.
Definiens’ takes a context-based, relational approach rather than a purely pixel-based pattern recognition approach. Definiens segmentation algorithms first group pixels into objects, called “image object primitives.” These objects are then merged into what the user recognizes as the microanatomy of the tissue, and then ultimately related to the super objects (white space, lumen, tissue, background, glands, etc.).
Because of this hierarchal relationship which links smallest elements in an image to the largest, Definiens provides a unique, and robust means of detecting and quantifying 100’s of relational attributes of the tissue, which could be related to clinical outcome; enabling more advanced questions to be asked of the underlying biology.
