inForm | Advanced Image

Analysis Software

Extracting crucial information from tissue images.

Extracting meaningful data from intact tissue is becoming evermore critical as researchers look for ways to characterize molecular activity of cells in their native microenvironments. In life sciences research and in pharmaceutical drug development, progress often depends on it. In translational oncology, it is central to target validation, trial design, patient selection, characterizing efficacy and response, and making correlations with clinical outcome.

inForm uses a learn-by-example interface, allowing you to transfer your knowledge of target tissue areas to the software by drawing training regions. Once trained, large numbers of images can be batch processed, extracting molecular signals from cells of interest in any number of images, at a rate of several images per minute. With Caliper’s multispectral technology, you can also spectrally ‘unmix’ multiple signals on a per-cell or per-object basis, capturing complex phenotypes.

INFORM

Automate image analysisinForm’s interface and underlying machine learning algorithms make it easy for you to teach the software to automatically perform image analysis steps that would otherwise have to be done manually, often saving days if not weeks of work. The computer can batch process 100s or 1000s of images at a rate of several per minute.

Improve objectivity and consistency of resultsAssessments can be more objective and consistent as they do not rely on visual inspection and interpretation, but rather on machine-based algorithms that employ Caliper’s intuitive tools for quantitating labels and stains.

Analyze tissue sections stained with most dyes, stains or labelsAnalyze tissue sections stained with conventional dyes such as H&E or Mason’s trichrome, as well as immunohistochemical (IHC) stains such as DAB or Vector Red, and immunofluorescent (IF) labels such as Alexa Fluor® dyes or QDots™.

Obtain per-cell and per-cell-com-partment multiparameter data Perform tissue-based cytometric analysis using Caliper’s multispectral imaging technology in combination with inForm. Reliably quantitate multiple markers apart from autofluorescence in objects, tissue regions, or cells. Extract flow-cytometry-like data while preserving the morphological context.

Tissue stained for PR (DAB) with counterstain (hematoxylin). Red and green user-defined regions teach the software to identify regions of interest; in this case, cancer-positive regions (red) versus stroma (green). Batch processing of images after training results in segmented target regions that can be further segmented at the cellular and sub-cellular levels. Extracted data can then be analyzed on a per-cell basis.

Hand-Drawn Training RegionsResults of Automated Segmentation

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Extracted Per-Cell Data

Segment difficult-to-detect regionsAutomatically segment a broad range of previously hard-to-detect objects or tissue regions, such as tumor, stroma, fibrosis, inflammation, necrosis, granuloma, vessels, or necrosis.

inForm automatically segments and quantitates hard-to-discern liver granulomas in conventional H&E stained tissue sections, avoiding the need for a costly and time consuming IHC step.

inForm analysis applied to immunofluorescent tissue section labeled for ER, PR and HER2, as well as DAPI. Data extracted from segmented images can be exported to generate flow-cytometry-like 3D scatter plots.

AFTERBEFORE

31% Granuloma

Multiplexed IF SectionAutomated Cell Segmentation

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ER PR

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Core (2,11)Core (10,3)Core (12,5)Core (7,7)

Per-Cell Multiparameter Data

INFORM

inForm offers key advantages:• Versatile - analyze any image, including IHC, IF, H&E, Trichrome, or other stains

• Easy to use - simply draw regions using the mouse to train the software

• Accurate training - train algorithms to accommodate tissue variability

• Multiplexing capability - Caliper’s multispectral imaging enables quantitation of multiple labels, and eliminates autofluorescence in IF

• Accurate quantitation - brightfield OD conversion tool allows for accurate quantitation of label intensity

• Quality control steps - unique review tools

• Portable and efficient - runs on a standard laptop or desktop PC

* Including color images extracted from any digital slide format, such as Aperio .svs or Nanozoomer .ndpi files.Product specifications subject to change. Refer to the CRi website for current information.

inForm SpecificationsImage formats Monochrome or Color* (TIFF, BMP, JPEG, PNG), Caliper Multispectral Images (.im3)

Segmentation types Tissue regions, objects, cellular and sub-cellular compartments

Max number of markers Extract as many signals per cell as there are spectrally unmixed components

Max number of classes per training set 8 (tissue regions or objects)

Max number of images per training setTypically up to 50, depends on image size and computer memory (Windows ® 7, 64-bit, 8 GB RAM)

Max number of images per batch set Unlimited

PC RequirementsWindows XP Pro or Windows 7, 32 or 64-bit, with Centrino or later processors (minimum 2 GB RAM, 8 GB preferred for Windows 7 64-bit)

Training processing speed Seconds per each image in the training set

Batch processing speed Multiple images per minute, typical

inForm Workflow an easy and quick process

Load training set. Draw regions around areas of interest. Hit the ‘Train’ button, and the software will converge rapidly (typically within seconds) on an algorithm. Any algorithm can be saved for future use.

inForm’s training interface allows flexible configuration of training and test sets, and the use of large numbers of images to capture the full range of tissue variability and staining .

1. Train 2. Batch 3. Analyze

Refine Since both staining and biology can be variable, a useful option exists to filter out unwanted small features and further refine segmentation, such as properly splitting nuclear material when nuclei from adjacent cells are touching, filling holes due to an incomplete counterstain, and smoothing region edges to desired amount. Iterations on algorithms with new training regions can be performed in minutes, providing reliable algorithms to support large studies.

Review Quickly review segmentation results from a batch run to flag data associated with images of tissues that were badly stained, prepared or imaged. Removing these images from the set helps to ensure data accuracy.

Using existing or newly created algorithm(s), load images from a study, and hit “Run all”. All images in the set will be segmented using the algorithm, often at a rate of several images per minute.

Measure percent positivity or h-score using inForm’s scoring tools, or export per-cell co-expression data using inForm’s extensive export features.

©2011 Caliper Life Sciences, Inc. All rights reserved. Caliper, the Caliper logo, Cambridge Research & Instrumentation, Inc., the

Cambridge Research & Instrumentation logo (CRi), Maestro, Nuance, Vectra, inForm and Dynamic Contrast Enhancement (DyCE) are tradenames and/or

trademarks of Caliper Life Sciences, Inc.

INF-BR-01 Feb11

Photography Credits • Breast tissue stained for PR using DAB, with a hematoxylin counterstain. Red and green user-defined regions teach the software to identify regions of interest; in this case, tumor regions (red) versus stroma (green). Batch processing of images after training results in segmented target regions that can be further segmented at the cellular and sub-cellular levels. Extracted data can then be analyzed on a per-cell and per-cell-compartment basis.

A Complete Product Portfolio

inForm

inForm image analysis software for automated quantitation of markers in cells and tissues. inForm addresses key data extraction challenges by using machine learning, that enables the expert to teach the software to identify and segment tissue areas or objects automatically.

Nuance

Nuance multispectral imaging systems for quantitative, multiple-marker analysis in immunohistochemistry and immunofluorescence microscopy. As biological imaging becomes more about studying complex systems revealed through the presence of more than one label, Nuance multispectral imaging systems enable higher degrees of multiplexing and reliability, producing clear and accurate images of each label, even though they are from a multi-labeled tissue section.

Vectra

Vectra slide analysis system for automated high-throughput slide imaging and analysis, the world’s only multispectral fluorescence- and brightfield-capable system. Vectra’s pattern recognition-based scanning automatically acquires high-resolution multispectral images of samples on microscope slides. Samples can be cultured cells, cell spreads, tissue sections or tissue microarrays, stained with standard stains such as H&E or trichrome or immunofluorescence and immunohistochemical techniques.

“The combination of multispectral imaging and pattern-recognition-based image analysis create a powerful tool for extracting key molecular information from tissue samples. The information revealed using Caliper’s inForm enables a wide range of clinically-significant research. ”

Dr. Massimo Loda, The Dana Farber Cancer Institute, Boston, MA

www.caliperLS.com