Division of Pathology Informatics -
Informatics Training

Pathology Informatics training is offered as part of an integrated training program within the Centers for Oncology and Pathology Informatics at the University of Pittsburgh. The Centers offer degree- and non-degree-seeking candidates formal training in the emerging discipline of medical informatics through academic programs in imaging research, computer-assisted decision support in pathology, processing and management of pathology data for research and clinical practice, tissue banking information systems and pathobioinformatics. The Centers support training programs for fellows, residents, visiting residents, graduate students and visiting faculty. Degree programs are available in Medical Informatics, Information Sciences and Telecommunications, Intelligent Systems, and Computational Biology.

Mission Statement

Oncology and Pathology Informatics is a developing discipline that focuses on the management and analysis of clinical and research oncology and pathology data using modern computing and communications techniques. The field includes the components of Medical Informatics and Bioinformatics that relate to clinical oncology and cancer research. Medical Informatics is the study and critical application of computing and communications technology to clinical practice and includes research related to production information systems in patient management, pathology, clinical trials, and the cancer registry; clinical workstations and graphical user interfaces; clinical decision support; medical error detection; clinical data mining; outcomes research; standard nomenclatures and natural language processing applied to medicine. Medical Informatics research is reshaping the way medicine is practiced and will provide the foundation for accurate, timely, effective and efficient care in the future. Bioinformatics focuses on basic research and seeks ways to optimize the storage, analysis and interpretation of complex biological data sets. Modern high-throughput technologies like micro-arrays and proteomics assays allow researchers using bioinformatics techniques to collect and analyze data on hundreds or thousands of genes and proteins simultaneously, which will lead to the discovery of important biomarkers, novel disease subtypes, new pathways of cellular communication and metabolism, and new, rationally-targeted therapies. Bioinformatics researchers also take advantage of the growing number of large-scale databases that warehouse genome and protein sequences to analyze and interpret structural and functional differences among such sequences, render and study the three-dimensional structure of interesting proteins, and relate data patterns to phenotypic expression and disease.

The Centers for Oncology and Pathology Informatics at the University of Pittsburgh train pathologists and oncologists to be leaders in the development and application of informatics in academic, industry or community practice settings. Because the field of informatics is broad, the training experience is flexible based on the trainee's goals and interests. Trainees may have clinical backgrounds in Pathology (three years of anatomic or clinical pathology, or four years of combined AP/CP training), equivalent training in another clinical specialty with a strong orientation to Oncology, or graduate training in biomedical science.

Degree and Certificate Programs in Medical Informatics

Certificates, Master's and doctoral degrees in medical informatics and bioinformatics are offered through the University of Pittsburgh School of Medicine in conjunction with the Department of Biomedical Informatics, the Intelligent Systems Program and the Cell Biology and Molecular Physiology Graduate Program. These nationally-recognized programs in informatics and bioinformatics provide stipend support though local and national training grants to qualified applicants. Faculty of the Centers for Oncology and Pathology informatics serve as core faculty and teach courses in these training programs. Trainees may enter the programs with faculty of the Centers as advisors, follow a curriculum targeted to their interests and carry out their independent research within the Centers for Pathology and Oncology Informatics.

Each of the collaborating programs offers a defined curriculum that includes didactic courses and independent research (see the respective programs' websites for descriptions of their curricula). All the programs offer Masters (2-year) and doctoral (4-5 year) degrees. In addition, the Department for Biomedical Informatics offers a unique 1-year Certificate in Medical Informatics curriculum that includes didactic courses and a faculty-supervised project.

Application: Candidates interested in certificate or degree training should contact the training program coordinator in the Centers for Oncology and Pathology Informatics (see contact information at the bottom of the page) and the coordinator in the appropriate collaborating program as listed on that program's Website. Application occurs through the collaborating program's admission process; important deadlines and acceptance schedules are noted on those programs' Web pages.

Research Fellowship Training

The Centers for Oncology and Pathology Informatics offer one- to two-year research fellowships in Oncology or Pathology Informatics to qualified applicants. The fellowship is designed to equip pathologists and oncologists with the skills required to lead information systems evaluation and implementation projects, incorporate informatics techniques into their own practice, and/or conduct academic work in the field of informatics. In some cases, research fellowships in informatics may be combined with clinical fellowships in other areas, such as Molecular Diagnostics or Dermatopathology, to provide a focus of informatics training in an area of clinical specialty.

The fellow has primary responsibility for designing and managing a project, with supervision by Centers faculty and support from Centers staff. Projects are chosen based on the fellow's training goals and level of computing expertise, and may include collaboration with informatics researchers and developers in other departments. Fellows present the results of their work in semi-annual seminars to the Centers and the Department of Pathology. Fellows are also expected to submit abstracts of their work for presentation at national conferences, and to submit manuscripts based on their work for publication in appropriate journals.

Fellows may be invited to participate in teaching pathology residents during the Core Informatics Rotation in the Department of Pathology, teaching graduate courses offered by Centers faculty, writing reviews with faculty members to address aspects of oncology/pathology informatics, and presenting in invited seminars given by Centers faculty to a variety of groups. A brief PDF file describing the fellowship is available by clicking here.

Additional training opportunities include courses and special seminars offered by the Center for Biomedical Informatics and the annual conference Advancing Practice, Instruction and Innovation through Informatics (APIII), which is managed by the Centers and held in Pittsburgh.

Applicants will typically have three years of anatomic or clinical pathology training, four years of combined AP/CP training, equivalent clinical training in an oncology-related medical field, or doctoral training in biomedical science.

Application: Applicants for the research fellowship should forward a current CV, a cover letter with a description of their training goals, interests and skills in informatics and at least three letters of recommendation to the Oncology/Pathology Informatics Training Program Coordinator (see Contact Information at the bottom of the page). Applications are considered at any time, but application 9 months to one year prior to the anticipated start date is recommended.

Resident Rotations

The Centers offer an intensive three week introduction to medical informatics for pathology residents once yearly. Residents from other clinical specialties or visiting residents from other training programs may participate in this rotation with permission from the Training Program Director. In addition, the Centers offer independent, project-oriented rotations ranging from one to six months in length for residents and medical students. The objectives and depth of these projects vary depending on the experience, interests and personal goals of the trainee. At a minimum, the rotator gains an understanding of the role of information technology in pathology and is exposed to computer networks, databases, imaging systems, laboratory information systems, the Internet and informatics research. Rotators routinely author academic papers and present posters at national informatics meetings.

Application: Residents interested in project-oriented rotations, or residents outside the University of Pittsburgh Pathology Residency Program who are interested in the introductory or independent rotations should contact the training program coordinator (below under "Contact Information"). Outside residents should also forward a current CV and a cover letter with a description of their training goals, interests and skills in informatics to the coordinator. Applications are considered at any time. For outside residents, application at least 6 months prior to the anticipated start date is recommended.

Conferences and National Meetings

The Centers host Advancing Practice, Instruction and Innovation through Informatics (APIII) each fall. This meeting is the premier national conference focusing on the application of informatics and advanced technologies to oncology and pathology research and practice. It also serves as the national meeting for the Association for Pathology Informatics (API). The meeting includes platform presentations of research and development in Oncology/Pathology Informatics, electronic poster presentations, breakout sessions and keynote presentations by nationally-recognized leaders in informatics. Trainees of the Centers attend the meeting at no cost and typically present their work in the platform or poster sessions.

The Centers also host monthly conferences in Pathology/Oncology Informatics and Bioinformatics and participate in weekly informatics conferences hosted by the Center for Biomedical Informatics and the Intelligent Systems Program. The various development groups within the Centers also meet weekly for journal clubs and project discussions.

Key Project Areas

A partial list of research areas available for trainee participation includes:

  • Telepathology implementation; network implications of robotic telepathology systems; collaborative telemicroscopy
  • Digitization, automated analysis and management of microscopic images for educational and diagnostic use
  • Clinical trials information management
  • Tissue banking information systems
  • Cancer registry development and data management
  • A multi-institutional archive of de-identified oncology patient information for research
  • Natural language processing and information extraction from pathology reports
  • Outcomes research and medical error reduction
  • Management and analysis of gene array data for oncology diagnosis and tumor profiling
  • Intelligent tutoring systems in pathology
  • Automated identification of clinically-relevant data patterns in the medical record
  • Clinical user interfaces that effectively communicate pathology data
  • Internet-based communication and support related to oncology care and clinical trial accrual
  • Development of information systems for specialty clinical laboratories

Support for Training

Trainees accepted into the training programs of the Centers for Biomedical Informatics, the Intelligent Systems Program and the Cell Biology and Molecular Physiology Graduate Program or the Oncology/Pathology Research Fellowships are provided stipends through those programs during training. Additional support mechanisms include:

Oncology and Pathology Informatics Center Facilities

The School of Medicine and the Department of Pathology have allocated approximately 2/3 of the third floor of the new Cancer Pavilion at UPMC Presbyterian-Shadyside Hospital for Pathology and Oncology Informatics. The Cancer Pavilion is next to Presbyterian-Shadyside Hospital in Pittsburgh's Shadyside district and is immediately across the street from the new University of Pittsburgh Cancer Center. The area currently houses 10 faculty (appointments variously in the Department of Pathology, Department of Medicine and the University of Pittsburgh Cancer Institute), 4 graduate students, 5 research fellows, 10 software engineers/developers (of various levels), approximately 15 project and system managers, approximately 10 hardware/software support staff and 5 database curators.

Teaching/Conference Space. There are three conference rooms and a computer lab within the facility. The conference rooms are equipped for multimedia and used regularly for conferences, graduate student training, weekly manager/staff meetings, and laboratory meetings. Each room contains a PC with monitor, a Sharp NoteVision projector and a Team Board, which is connected to the computer, support for teleconferencing, table seating for 12 and additional seating for 16-20. The rooms are also equipped with full audio-visual equipment including two VHS video recorders and a wireless microphone for speaking presentations. There is also a slide projector with a large pull down projection screen. The computer laboratory houses 12 student PCs and an instructor PC with below-desk monitors. The instructor PC is connected to a Team Board.

Staff, Student and Faculty Office Space. The north end of the facility contains the front office/receptionist area and cubicles for administrative staff. This is one of two card-access points of entry to the area. The reception area also houses the fax machine, office supply cabinet, and a common laser printer. Faculty and administrative support offices occupy the north end of the floor around the reception area. Nine student carrels are adjacent to the faculty offices. A shared color laser printer, large format poster printer and copy machine are nearby. Senior programmers and additional faculty occupy offices in the south end of the floor. The entire western half of the floor (1600 square feet) houses cubicles for 56 system managers/software engineers/developers and database managers. Each subdivision in the cubicle area has a dedicated networked laser printer.

Telepathology Laboratory. The Laboratory for Telepathology and Imaging consists of three related labs within the Centers facilities. 1) The Whole Slide Imaging Lab contains an Aperio Scan Scope and InterScope Excellator. The Whole Slide Scanners are connected to the Imaging Server, which has multi terrabyte storage. The Imaging Server is also connected to a DVD juke box for backup. 2) The Multi-Spectral Imaging Lab contains both 16 band and 6 band imaging systems. The 16 band system is equipped with a robotic microscope and a digital camera with 2k x 2k resolution. This lab also contains a multimedia editing computer for the Webcast Conferencing System. 3) The Telepathology Lab has a variety of telepathology systems, including a Dynamic Robotic telepathology system supporting Internet or ISDN use, a TV Conference system, a Static Image Telepathology System, a networked camera attached to a Leica microscope and a Nikon CoolScope. All systems utilize image enhancement, image analysis and telepathology software custom-developed at UPMC. The laboratory is also designed to simulate telepathology between remote and local sites using several additional computers which are prepared for demonstrations and training.

User-Centered Informatics Technology Evaluation (UCITE) Laboratory. The UCITE Laboratory serves as a multi-purpose space for design, development and evaluation studies. The space contains an interactive Team Board, 2 workstations, locked cabinets for data and media storage, a microscope with video-capture and compression capabilities, and table and chairs suitable for interviews and focus groups. The workstations are equipped with video capture and editing software. Additional equipment includes a laptop computer, LCD projector, as well as hardware and software for digital audio, digital video, and still image acquisition. Workstations are mapped to a central Network Attached Storage (NAS) device permitting archiving of video and audio data. The room is easily re-configured to support a wide variety of types of user-centered activities.

Server Room. The server room is adjacent to the developer cubicles and houses 7 production and research servers. It houses two Dell Poweredge XE 590 servers with 6 GB of storage and 196 MB RAM. These servers are used as Microsoft Windows NT server and as an Application server. Also, there is one Dell Poweredge XE 590 server with 45 GB of storage and 196 MB RAM and serves as the Real Audio and Video, and one Dell Poweredge 2200 Dual Pentium II 333MHz with 9 GB running RAIDS and 256 MB Ram, and one Compaq DeskPro 50M 486/66MHz with one GB of storage and 32 MB RAM which serves as a backup server with Novell Netware operating system. There is also one Apple Macintosh dual G5 2GHz and one Macintosh G5 1.8GHz, both with 1 GB RAM and 250 GB storage, which are used in research and development. The server room is secured with card access.

General Computing Resources. The combined total of desktop computers are Apple (7), Compaq (44), Dell (39), DTX (1), Micron (1), Gateway (2). A typical desktop is a Dell Optiplex 590 with 256 MB RAM and 6 GB of storage linked to a 17-inch NEC Multisync 5FG monitor). All are P3s or P4s. All PCs are connected to Hewlett Packard LaserJet 4 printers and to 10BASE-T Ethernet connections and Iomega Zip Drives, speakers, CD-ROM, and 8-MG video card. There are total of 5 networked Hewlett Packard LaserJet 5 printers and one networked Hewlett Packard LaserJet 5 color printer.

Lunch Room. The Lunchroom includes a kitchenette (with refrigerator, microwave, coffee machine, sink and water cooler), and a separate eating area with table and chairs to accommodate approx. 20 people.

Contact Information

Douglas J. Hartman, MD
Director of Pathology Informatics Fellowship Program
Rm. A610
Presbyterian University Hospital
200 Lothrop Street
Pittsburgh, PA 15213
Phone: (412) 864-3552
Email: hartmandj@upmc.edu