pathology

1. Pathology informatics
Guide – Lt Col Sonia Badwal

2.  Introduction
 Definitions
 Pathology Information System
 Basic design criteria
 Additional features
 Laboratory Information System
 Role of Informatics

3. Introduction
 20th
century - histologic evaluation of tissue by
pathologist - single most information rich and
decisive, diagnostic assessment tool available

4. Introduction
 21st
century
 Information & communication technologies - changes in
health services
 Parallel methodologies - gene analysis, molecular basis
of disorder & drug susceptibilities
 Provide information rich data streams to aid diagnoses
& treatment

5. Challenge to historic role of pathologist
 To meet these challenges - need to merge these
methods & other data stream with traditional approaches
of tissue assessment
 Requires development of a pathology information system
 Data integration from diverse modalities , data
presentation & decision support
 These activities fall under the emerging field of
Pathology Informatics

6. Definition
 Informatics:
 Study of application of
Information Technology
 Acquiring, storing,
processing & retrieving
analysed data
 Convert data into
information
 Medical Informatics: Study
of application of information
technology to medical
science & health care
delivery

7. 7
Components of Medical Informatics
 Information Technology
 Health care
 Research
 Education
 Fundamentals
 Clinical Information
Management
 Knowledge Management
 Decision support
 Communication

8. 8
Medical Informatics
Knowledge
Management
Clinical Information
Management
Communication Decision Support

9. Current vs. Integrated Approach
Current Method: Integrated Approach:
Medical records written on
paper forms by doctors,
some information stored in
private database
Data typed into electronic
forms which are
connected to a central
database or network of
databases
Pt’s original records stored at
care facility where treatment
took place
Records must be manually
faxed if needed by a different
care facility.
Data stored in a protected
database which can be
accessed remotely with
correct authorization

10. Pathology Informatics
 Discipline & practice of
using electronic
information systems
 To facilitate, promote &
advance practice of
pathology
 patient care
 understanding of
disease
 education

11. Pathology Informatics
 Laboratories & Anatomic pathology - digitized /
automated
Information derived from various sources
Standardized & coded "machine consumable" data
Integrated reports communicate with multiple hospital
systems

12. Pathology Informatics
 Data need to be exchanged between multiple,
heterogeneous systems
 For representing & communicating information – well
defined standards needed
 Standards needed for :
 Transferring patient data across different systems
 Representing medical knowledge that can be reused

13. Standardized Nomenclatures

14. SNOMED
 Systematized Nomenclature of Medicine
 Coded medical nomenclature, which allows recording of
all disease entities regardless of prevalence
 Developed & supported by College of American
Pathologists
 Comprehensive clinical terminology that is used to:
 Code
 Retrieve &
 Analyze clinical data

15. ICD-10
 International standard classification for all
general epidemiological, many health
management purposes and clinical use
 3-digit codes
 Used in ~110 countries for cause of death
reporting & statistics

16. ICD-10

17. Logical Observations, Identifiers,
Names and Codes (LOINC)
 Database & universal standard for identifying medical
laboratory observations
 Created in response to demand for an electronic
database for clinical care & management
 Database has expanded to include medical & laboratory
code names
 Purpose - assist in electronic exchange & gathering of
clinical results (such as laboratory tests, clinical
observations, outcomes management and research)

18. Information systems in pathology
 Rapid pace of workflow - efficient methods to collect,
store, display & distribute data generated
 At one end of information system - specimen received
& accessioned & at other end analyzed into
‘pathology report’
 Report must be accessible to all those who need it,
ensuring confidentiality
 Pathology Information System – Foundation for critical
information handling

19. Information systems in pathology
 Pathology laboratory information system –
Comprehensive software that manages laboratory
workflow & reporting
 Properly implemented enhance
 Ability to store, organize & retrieve prodigious
amounts of information
 Efficiency of surgical pathology laboratory
 Improve quality of services
 Monitor quality assurance parameters
 Aid in research

20. Information systems in pathology
 First such software
developed at
 Tufts University
(SURGPATH)
 Massachusetts’s
General Hospital
(CAPER)
 Yale University
(CoPATH)

23. Basic design criteria
 To allow pathologist
to work independently
of the computer
 Elimination of
redundant data entry
 Real time integration
of data from all
aspects of diagnostic
pathology

24. Basic design criteria
 On-line permanent and
safe storage of all
primary data
 Rapid response time
 Flexible & easily
modified design

25. Automated Anatomical Pathology System
 Operates on computer dedicated to anatomic pathology
 Terminals linked to system installed at foll places:
 Staff offices
 Sign out areas
 Secretarial areas & Administration
 Cytology
 Histology
 Surgical pathology gross room
 Autopsy room
 Similar terminals placed throughout hospital

26. Information System

28. Organization
1. Surgical pathology
2. Cytology
3. Autopsy
4. Department wide options
5. System manager
6. Histology & IHC laboratory
7. Molecular genetic laboratory
8. Miscellaneous

29. Surgical pathology
 Accomplishes all tasks performed in surgical pathology
laboratory
 On accessioning a new specimen
– information on the patient, specimen, submitting
physician etc. collected
 Information on ‘type of specimen’ captured - allows
computer to obtain preliminary information

30. Surgical pathology
 Specimen of breast resection
 Entering ‘BRE’ – computer responds by asking the user
to select from:
1. Breast: Biopsy
2. Breast: Resection for Cancer
3. Breast: Reduction Mammoplasty( Not Cancer)
 To anticipate
 proper procedure for grossing specimen
 Generate customized data labels
 Provide specific instructions to technicians & pathologist

31. Surgical pathology
 All information & protocols generated by selection of
‘specimen type’
- derived from user defined ‘dictionaries’
 All text entries ( e.g gross description, final diagnosis)
- made directly in appropriate data field
- simple text editor/word processor
 All aspects of the case - edited simultaneously by
different users

32. Surgical pathology
 All text fields allow
 free text entry or
 choices of user defined ‘canned’ text
 forms & check lists for standardized reporting
diagnoses for major tumor types
 Diagnoses entered may be
 ‘Preliminary’ report – cases requiring special studies;
reads as – ‘poorly differentiated carcinoma, specific
type pending IHC’
 ‘Final’ report

33. Surgical pathology
 Many standard reports generated by system – 2 most
common being:
 Working Draft
 Printed on completion of gross dictation
- contains synopsis of all previous/current related clinical
history
- cytology & other data
- full text of gross description
 Pathologist may record diagnosis on this sheet or
enter it directly into terminal
 Finished format report
 Signed electronically & made immediately
available

34. Surgical pathology
 Standard Inquiry –displays full text of
 Gross description
 Diagnosis, amendments to diagnosis
 Information on special procedures
 Date each task completed
 Other data - gross photograph taken
- tissue saved
- special fixatives used
- status of slides preparation

35. Surgical pathology
 For use outside department - separate inquiry options
 simplified presentation of diagnostic information
 other options provide detailed information on status of
microscopic slides & special stains for each case

36. Cytology
 Similar to functioning of surgical pathology section
 Major difference
 makes extensive use of case/type- specific
questionnaires
 only relevant questions asked at time of accessioning
 On accessioning slides - labels automatically generated
contg:
 Patient name
 Slide designation
 Cytology number

37. Cytology
 Reporting cytology specimens facilitated by using
‘checklist’
 Cytotechnologist selects predefined features recognized
in smear
 From these checklists computer automatically SNOMED
codes specimen
 Decides which specimens reqd to be reviewed by
pathologist( based on predefined criteria)
 Generate a completed full text report
 Quality control review - captures a percentage of cases

39. Autopsy
 Complete morgue registration system
 Handles all aspects of autopsy report preparation
 Unlike surgical/cytology section - unlimited text &
‘canned’ text entries
 ‘Specimen type’ concept also used in autopsy section
- To generate case specific autopsy worksheets
 Provide a measure of increased quality control in
autopsy room

40. Department - wide options
 General search capabilities of system in this section
 Two search options provided –
 Disease Search option
 Report Generator

41. Department - wide options
Disease Search option
 Involves finding of cases with certain diagnoses or
combination of diagnoses
 Done using SNOMED search option

42. Department - wide options
Report generator
 Software package - arbitrary search over any of data
items captured in system
 Output format – user defined
 Any type of report can be compiled with this option

43. Systems manager
 Allows editing of all dictionaries used in system
 Provides a number of other maintenance &
administrative features
 All transactions in systems manager leave an audit trail
 Access to this section strictly limited to staff members

44. Histology & IHC laboratory
 Handles all functions related to preparation of slides from
handling of specimens
 Begins in grossing room
 Pathologist enters directly into the terminal
 Information on - number of blocks & tissue
pieces submitted
- any special request for
stains, recuts etc
 For routine specimens – information needed is already
anticipated by computer based on ‘specimen type’, only
needed to be verified

45. Histology & IHC laboratory
 All worksheets in histology lab
 Generated automatically from entries in grossing
room
 Contain all information necessary for slide preparation
 All requests for special stain, recuts etc - entered directly
into system & appear on ‘SPECIAL STAIN’ log
 All slide labels printed automatically
 For special stains - labels contain type of stain & date of
procedure

46. Molecular genetic laboratory
 Provides a separate registration system
 Fully integrated with surgical pathology & cytology
sections
Miscellaneous
 Contains items such as grading & staging manual for
major tumor types

47. Additional features
 Digital pathology
 Telepathology
 Digital speech recognition

48. Digital Pathology
 Whole slide imaging
(WSI), digital imaging,
virtual slides, virtual
microscopy
 Use of computer
technology to convert
microscopic images
into digital images

49. Digital Pathology
Mechanical
scanner
Light
source
SLIDE
Imaging
optics
Digital
image
sensor
Image
Processing
software Display
READERIMAGE
DATA FILES
Conventional
optical microscope

50. Digital Pathology
 Scan - Digital slides
created using scanning
device
 View - Digital slides
viewed via viewing
software on computer
monitor

51. Digital Pathology
 Manage - Digital slides
maintained in information
management system that
allows for archival &
retrieval
 Analyze - Image analysis
tools for objective
quantification measures

52. Digital Pathology
 Integrate – Workflow
integrated into institution's
operational environment
 Sharing - internet
information sharing for
education, diagnostics,
publication & research

53. Utility of Digital Pathology
 View images even over large distances via the Internet
 Share exactly same image with colleagues at same time
 Clinico-pathological conferences without glass slides
 Automate & optimize pathology workflow

54. Digital Pathology Applications
1. Education and Training
- allows viewing of
virtual slides by large
numbers of students
simultaneously
- advantage- all
students view exactly
the same slide at the
same time

55. Digital Pathology Applications
2. Diagnosis
- easy consultation
(without any need to
physically transport the
slides)
- rare diseases
- Instant frozen section
diagnosis over the
Internet

56. Digital Pathology Applications
3. Tissue Micro Array (TMA)
- scanner & TMA software
- segment TMA slides into
cores
- Assist in manual, semi-
automatic / automatic
scoring
- Link individual scores with
patient ID in database
- Perform data mining and
statistics in huge databases

57. Digital Pathology Applications
4. Image Analysis
- Quantify nuclear, cellular or membrane markers
- Count cells, nuclei or more complex structures
- Use powerful morphometry tools
5. Archiving
- Virtual slides - stored locally on computer systems
- Allows easy retrieval for retrospective studies

58. Virtual Microscopy ideal method for
following applications
 Remote diagnostic viewing
 Clinical remote consultation
 Group presentations and discussion
 Student education
 Case libraries and tissue databanks
 Large-volume software-aided image analysis

59. Telepathology
 Practice of pathology at a
distance
 Uses telecommunications
technology
 To facilitate transfer of
image-rich pathology data
b/w distant locations
 For the purposes of
diagnosis, education &
research

60. Telepathology
Divided into three major
types:
 Static image-based
systems
- benefit - most
reasonably priced &
usable systems
- drawback - capture a
only a selected subset
of microscopic fields
for off-site evaluation

61. Telepathology
 Real-time systems
- robotic microscopy systems & virtual slides
- allow consultant pathologist to evaluate HPE slides in
entirety, from a distance
- consultant actively operates robotically controlled
motorized microscope
- located at a distant site—changing focus, illumination,
magnification, & field of view—at will
- perform best on local area networks (LANs)

62. Real time Telepathology

63. Telepathology
 Virtual slide system
- utilize automated digital slide scanners to create digital
image
- stored on computer server & can be navigated at a
distance, over the Internet using a browser
- emerging as the technology of choice for telepathology
services

64. Telepathology - Virtual slide system

65. Uses & Benefits of Telepathology
 Wide spectrum clinical applications
 diagnosing of frozen section specimens
 primary histopathology diagnoses
 second opinion diagnoses
 subspecialty pathology expert diagnoses
 education, compentency assessment & research

66. Digital speech recognition
 Converts spoken words
to text
 “Voice recognition" -
recognition systems
trained to a particular
speaker’ voice
 Front-end or back-end of
medical documentation
process

67. Digital speech recognition
 Front-End SR
- provider dictates into
speech-recognition
engine
- recognized words
displayed right after they
are spoken
- dictator responsible for
editing & signing off on
document

68. Digital speech recognition
 Back-End SR / Deferred SR
- provider dictates into digital dictation system
- voice routed through speech-recognition machine
- recognized draft document routed to the MT/editor
- MT edits draft & finalizes report

69. Digital speech recognition
 Electronic Medical Records (EMR) - more effective &
performed easily when in conjunction with speech-
recognition engine
 Searches, queries, & form filling - all may be faster to
perform by voice than by using a keyboard

70. Laboratory Information System
Includes
 sample management,
 data acquisition
 data processing
 reporting
 scientific data
management

71. Lab Information System - Key Steps
 Register patient - Patient record created in LIS
 LIS automatically receives data from hospital registration
system (when pt admitted)
 Order tests - Physician orders tests to be drawn as part
of laboratory's morning bld collection
 Order entered into the HIS & electronically sent to the
LIS

72. Lab Information System - Key Steps
 Collect sample - Before collection, LIS prints list of all
pts & appropriate number of sample bar code labels for
each patient printed
 Each bar code has - patient ID, sample container type
and laboratory workstation
 Another approach - patient caregivers/nurses to collect
sample
 Prior to collection, bar code labels printed (on demand)
at nursing station on LIS printer

73. Lab Information System - Key Steps
 Receive sample - on arrival in laboratory, status to be
updated in LIS from ‘collected’ to ‘received’
 Can be done by scanning each sample container's
bar code ID into LIS
 Once sample ‘received’ - LIS transmits test order to
analyzer
 Run sample - sample loaded onto analyzer & bar code
is read
 analyzer knows which tests to perform on patient – as
test order from LIS already been received
 No worklist needed

74. Lab Information System - Key Steps
 For manually performed tests - technologist prints
worklist from LIS - contains list of patients & tests
ordered on each
 Next to each test is a space to record result
 Review results - analyzer produces results & send to
LIS
 Results viewable only to technologists as they have not
been released for general viewing
 LIS can be programmed to flag critical values

75. Lab Information System - Key Steps
 Release results - technologist releases results
 Unflagged results usually reviewed & released at
same time
 LIS can be programmed to automatically review &
release normal results or results that fall within a certain
range
 Latter approach reduces number of tests that
technologist has to review
 On release
- Results automatically transmitted to HIS
- Physician can view results on HIS screen

76. Pathology Informatics - Specific tasks
1. Modification of existing information systems –
 Integrating data with clinical laboratory , radiology,
pharmacy, medical records & all systems collecting
information of medical relevance
 Pathology systems - properly formatted, organized &
highest stds of security

77. Pathology Informatics - Specific tasks
2. Adoption of methodologies & techniques –
 Quantitative & rationalized indexing of primary data
 Data collection, organization, interpretation,
presentation, & decision-making algorithms
3. Expanded recognition & support for Path Informatics as
legitimate subdiscipline of pathology

78. Role of informatics & pathologist

79. Role of informatics & pathologist

80. Conclusion
 Pathology Informatics – moving rapidly to keep
up with advances in pathology diagnostics
 Facilitate in quality assurance, internal
workflow, clinical services & academic
endeavors
 Rapid advances occurring in the fields of digital
imaging & telepathology
 An integrated pathology workstation with
capability of photographing, scanning &
sharing images is the future of pathology

81. References
 Rosai and Ackerman’s Surgical pathology 9th
volume. Chapter 1-
Introduction:14-22
 Modern Surgical Pathology 2nd
edition. Chapter 4- Anatomic
Pathology Information Systems:36-47
 Henry's Clinical Diagnosis and Management by Laboratory
Methods, 21st
edition.Chapter11:214-230
 Sinard JH, Morrow Jon S.Informatics and Anatomic
Pathology:Meeting Challenges and Charting the Future. Hum
Pathology 2001,32:143-148
 Reinhold Haux. Health information systems- past, present, future.
International Journal of Medical Informatics 2006,75: 268—281
 Elizabeth A. Krupinsnki. Optimising the pathology workstation
“cockpit”:Challenges and solutions International Journal of Medical
Informatics 2010,1: 14 -19