| Literature DB >> 30984469 |
Famke Aeffner1, Mark D Zarella2, Nathan Buchbinder3, Marilyn M Bui4, Matthew R Goodman5, Douglas J Hartman6, Giovanni M Lujan7, Mariam A Molani8, Anil V Parwani9, Kate Lillard10, Oliver C Turner11, Venkata N P Vemuri5, Ana G Yuil-Valdes8, Douglas Bowman10.
Abstract
The advent of whole-slide imaging in digital pathology has brought about the advancement of computer-aided examination of tissue via digital image analysis. Digitized slides can now be easily annotated and analyzed via a variety of algorithms. This study reviews the fundamentals of tissue image analysis and aims to provide pathologists with basic information regarding the features, applications, and general workflow of these new tools. The review gives an overview of the basic categories of software solutions available, potential analysis strategies, technical considerations, and general algorithm readouts. Advantages and limitations of tissue image analysis are discussed, and emerging concepts, such as artificial intelligence and machine learning, are introduced. Finally, examples of how digital image analysis tools are currently being used in diagnostic laboratories, translational research, and drug development are discussed.Entities:
Keywords: Artificial intelligence; computational pathology; digital pathology; image analysis; quantitative image analysis; whole-slide imaging
Year: 2019 PMID: 30984469 PMCID: PMC6437786 DOI: 10.4103/jpi.jpi_82_18
Source DB: PubMed Journal: J Pathol Inform
Figure 1Hematoxylin and eosin-stained image analyzed using the “cell detection” algorithm in QuPath (open-source tool). Nuclear segmentation, depicted as red outlines, was fragmented in the rightmost image by setting the noise reduction Gaussian filter σ = 1.0. Conversely, nuclear oversegmentation was achieved by setting σ = 2.5. Black arrows in the left image denote examples of single objects that consisted of multiple nuclei
Figure 2Sample hematoxylin and eosin images obtained from six sources designated on the right depict different color attributes commonly encountered when viewing digital images of slides across laboratories or across imaging modalities
Figure 3(a) A mouse xenograft tumor sample is stained with hematoxylin and Ki67 (DAB). (b) An enlarged region is shown where nuclei are stained blue and Ki67+ cells are brown. (c) A pathologist-trained random forest classifier is developed to identify tumor (green), stroma (blue), necrosis (red), and glass (gray). (d) The algorithm parameters are fine-tuned with the pathologist's input to optimize the nuclear segmentation and to define intensity thresholds to categorize the expression into four bins: 0+ (blue), 1+ (yellow), 2+ (orange), and 3+ (red)
Figure 4Digital pathology image analysis in spatial context reveal biomarker and cell heterogeneity. (a) The inset digital slide with DAB-stained biomarker (brown) was analyzed. Cells identified in the analysis were plotted spatially as a dot plot and each cell “dot” color coded according to the optical density of DAB stain in that cell. Cells in “cooler” colors (blues and greens) have lower stain optical density compared to cells in “warmer” colors (yellow, orange, and red). (b) Tumor cells and immune cells (DAB-positive) identified by image analysis were plotted spatially and analyzed to quantify immune cells within 30 μm of tumor cells (proximal immune cells). Tumor cells are colored blue, proximal immune cells are colored red, and nonproximal immune cells are green. The distance between tumor cells and proximal immune cells are recorded to create a histogram (inset, bottom right) and are connected by nearest neighbor lines in the dot plot
Figure 5Digital pathology image analysis in the pancreas and brain. (a) Islets stained with antibodies against insulin (red stain) and glucagon (brown stain) in digital slides. Analysis shown bottom left quantifies number of islets that are of islet (orange area in markup) and number of cells that are positive for insulin (red cell markup), glucagon (green cell markup), both (yellow cell markup), or neither marker (white cell markup). (b) Identification of beta-amyloid plaques in brain sections. Slides are probed with antibodies against beta-amyloid (purple) and vessel endothelial marker (brown). Digital image analysis shown bottom right quantifies density, diameter, and area of vessels (red markup) and plaques (green markup), and colocalized area (yellow markup)
Role of image analysis in different phases of drug development
| Phase | Image analysis role |
|---|---|
| Discovery phase | • Quantitative analysis of target and pathway inhibition biomarkers using xenografts and |
| • Measurement of target expression and specificity using TMAs and other high-throughput approaches | |
| • Correlative analysis (e.g., efficacy) for identification of potential companion or complementary biomarkers based on animal models | |
| Preclinical studies | • Animal models and safety assessment (non-GLP): Quantification of hypertrophy, steatosis, fibrosis, and other readouts using traditional image analysis approaches |
| • Quantification of organ morphology using machine learning-based tissue classification (e.g., islets in pancreas and glomeruli in kidney) | |
| • Additional studies in different animal models to identify potential clinical biomarkers | |
| Clinical trials | • Analysis of biomarkers used for patient stratification and prediction of therapeutic response |
| • Deep learning approaches to identify classifiers for patient stratification and prediction of therapeutic response |
TMA: Tissue microarray , GLP: Good laboratory practice
Pros and cons of open-source versus commercial digital image analysis software
| Open source | Commercial | |
|---|---|---|
| Cost | Free | Moderate to expensive |
| Technical support | Limited, provided by email and chat groups | Guaranteed support for customer issues |
| License | No software license necessary, and installation and updates administered by user | Software license required; installation and updates administered or supported by vendor |
| Viability | Life of software and new development at risk of open-source provider - potential short-term viability | Life of software and new development at risk of vendor - though typically longer-term viability |
| Fixing issues | Rapid, collaborative response to troubleshoot malfunctions | Only vendor experts can troubleshoot malfunctions |
| Software application training | Limited hands-on training, but online resources often exist | On-site and online training provided by vendor |
| Image file compatibility | May be compatible with a variety of image formats | May have limited compatibility |
Important considerations for choosing digital pathology image analysis software
| Consideration | Key question(s) |
|---|---|
| Application | Will the software be utilized for optimization of clinical/diagnostic workflow, basic research, or research in a regulated environment? |
| User-friendliness | Is it easy and convenient to interact with the software interface? |
| Training requirement | What level of expertise is required to operate the software? |
| What duration of staff training will be required to effectively utilize the software? | |
| Performance: Speed and capacity | What is the speed and capacity of the analyzer? |
| How long does image processing take for a single image? Can the user increase throughput by utilizing distributed computing? | |
| Resources | What additional resources (e.g., technologists, hardware, laboratory footprint, IT infrastructure, etc.,) are required for the optimal function? |
| Technical support | Where is the nearest customer support location or time zone? |
| In what manner, and how quickly do customer support personnel respond to issues? | |
| Licensure | Is a paid license required? |
| Per user, per instance, or per laboratory/research unit? | |
| File compatibility | In what file format can data be exported? |
| Is the software compatible with multiple image file formats from various whole-slide scanners? | |
| Including bright-field and/or fluorescent scans? | |
| Data storage | What is the average file size of an analysis run and data packages created? |
| Cloud storage provided by vendor or own internal storage solution required? | |
| Servicing | How are hardware and software malfunctions managed? |
| How often are software updates required? | |
| Cost-benefit analysis | How much will the image analysis solution cost? |
| Can individual modules be acquired based on needs, or will a full package need to be | |
| purchased? | |
| What is the cost of servicing/updating the software? | |
| What are the terms of the warranty? | |
| What is the cost of all additional resources required for optimal use of the software? | |
| After how much time will use of the analyzer result in a net gain? | |
| Will there be enough use cases to justify investment into equipment, infrastructure and staff, or would outsourcing to a service provider be more economical? |
IT: Information technology