Informatics, digital & computational pathology

Laboratory information systems


Last author update: 15 February 2023
Last staff update: 16 February 2023

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PubMed Search: Anatomic pathology laboratory information systems

Ugochukwu John Jonah, M.B.B.S.
Anil Parwani, M.D., Ph.D., M.B.A.
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Cite this page: Jonah UJ, Parwani A. APLIS. website. Accessed October 3rd, 2023.
Definition / general
  • A laboratory information system (LIS) is a computer software that processes, stores and manages data from all stages of medical processes and tests in the following ways:
    • Coordinates inpatient and outpatient medical testing
    • Contains features that manage patient check in, order entry specimen processing, result entry and patient demographics

      APLIS workflow

    • Tracks and stores clinical details about a patient during laboratory visit

      LIS assisted transactions

    • Keeps all patient information stored in a database for future reference
    • Electronic submission of lab test results to public health agencies and the incorporation of clinical lab test results into a certified electronic health record (EHR) system (see Videos) (TechTarget Network: Laboratory Information System [Accessed 10 February 2023])
    • Laboratory information system (LIS) is remarkably like laboratory information management system (LIMS) except that the later, in addition to healthcare, is also deployed in multiple nonmedical settings (TechTarget Network: Laboratory Information System [Accessed 10 February 2023])
    • Anatomic pathology laboratory information systems (APLIS) are also typically networked to other external information systems, such as hospital information systems (HIS)
      • The HIS makes use of the admission discharge transfer (ADT) interface
  • Anatomic pathology (AP) is the subspecialty of pathology that:
    • Deals with the examination and microscopic study of organs and tissues removed for biopsy or during postmortem examination
    • Interprets the results of the studies above
    • Involves the use of the naked eye for examination (gross pathology and by autopsy)
    • Involves the use of microscopy (histopathology)
    • Involves the use of electron microscopy (ultrastructural pathology) and other methods (The Free Dictionary by Farlex: Anatomic Pathology [Accessed 10 February 2023])
Essential features
  • LIS integration into pathology laboratory activities comes with the following features (Trust Radius: Laboratory Information Management Systems [Accessed 10 February 2023]):
    • Enhances efficiency in the laboratory by reducing manual procedures
    • Allows for the storage of comprehensive patient profile for extended periods
    • Generates easy and accurate billing of patient's charges
    • Makes use of barcode generation, printing and reading for the efficient identification of tubes, samples, documents, slides, etc.
    • Makes use of a built in bidirectional interface that allows for efficient interactions between the information system and the clinical instrument required (see Videos)

      LIS based bidirectional interface

  • Components of APLIS are detailed below and are summarized in Table 1 below (see Diagrams / tables)
  • Hardware: this refers to any physical device that interfaces electronically with the APLIS application, including (Adv Anat Pathol 2012;19:81):
    • Server computer
    • Client computer
    • Input / output devices of the computer
      • Keyboards, mice, monitor, etc.
      • Document scanners
      • Digital cameras
    • Printers (papers, labels, tissue cassettes)
    • Network hardware
      • Cables
      • Routers
    • Barcode scanners
    • Gross pathology examination stations
    • H&E autostainers
    • Whole slide imaging scanners: this requires a large amount of storage data and bandwidth (Adv Anat Pathol 2012;19:81)

      APLIS hardware components

  • Operating systems (OS)
    • OS are the point of human computer interface (Adv Anat Pathol 2012;19:81)
    • There are 2 categories:
      • Frontend operating system involving interactions with a human being
      • Backend operating system, which includes the following:
        • Databasing
        • Web serving
        • Storage
        • Networking
        • Other automated processes not requiring human intervention
      • Most modern OS combine both categories but are optimized toward one end or the other
      • Examples of OS include:
        • Microsoft
        • Windows
        • Mac OS X
        • Linux
  • APLIS software
    • Software used in APLIS comes as drivers that provide an interface between an operating system and a peripheral device (Adv Anat Pathol 2012;19:81)
    • These drivers are extremely operating system specific
    • Third party software known as middleware can be integrated into LIS, enabling the performance of the following functions:
      • Lab operation improvements; examples include:
        • LIS operations support (Microsoft Word and Excel, Crystal Reports)
        • Data transmission (Forward Advantage, LabDE)
        • Storage solutions (HP StorageWorks EVA8000)
        • Virtual applications support
        • Legacy apps
        • Web based cloud management (VMWare, Citrix)
      • Workflow improvements; examples include:
        • Instrument middleware
        • Tracking solutions
        • Remote system monitoring (Realtime)
        • Digital image management (Apollo PathPACS)
      • Quality improvement; examples include:
        • Quality assurance programs for platforms like Altosoft Insight, IBM Cognos
      • Service improvements; examples include:
        • Patient and client services (web portals)
        • Outreach connectivity tools (e.g., Lifepoint, Atlas, CareEvolve, etc.)
      • Revenue improvements (e.g., interfaced billing management tools)
  • Database management systems
    • A database is a collection of data in digital form, organized to model information of interest (Adv Anat Pathol 2012;19:81)
    • Examples include:
      • Spreadsheet containing patient data
      • Spreadsheet containing information on all surgical pathology slides signed out in a laboratory in a month
    • Database management system (DBMS) refers to the software used to manage a database and its data structures
    • DBMS allows users to create, update, delete and retrieve the data or the records stored (EDCUBA: What is DBMS? [Accessed 10 February 2023])
    • Thus, DBMS users can manipulate data to fit their individual requirements
    • In fact, DBMS is considered the heart of APLIS
      • An example is a Microsoft Excel application that can be used to manage information on the spreadsheets above
    • DBMS can be classified into 4 models detailed below:
      • Flat model makes use of single 2 dimensional tables stored in individual files (e.g., Microsoft Excel spreadsheet, tab separated values [TSV] or comma separated values [CSV])
      • Hierarchical model uses a tree-like model in which the parent nodes have multiple branches (children's nodes) but each child node has only 1 parent (e.g., MUMPS, eXtensible Markup Language [XML]) (J Am Med Inform Assoc 2002;9:307)
      • Relational model is the dominant model at present and uses 2 dimensional tables linked to each other by way of special key values (e.g., Microsoft SQL server, oracle database) (EDCUBA: Data Models in DBMS [Accessed 10 February 2023])
      • Dimensional model is a specialized form of relational model that uses 3 dimensional instead of 2 dimensional tables (e.g., Altosoft Insight, IBM Cognos)
  • Document / procedure management systems (DMS)
    • DMS can be employed by an AP laboratory to track, share and store relevant documents (Smartsheet: Guide to Document Management Systems [Accessed 10 February 2023])
    • DMS can also be possibly integrated into the laboratory's workflow process or project management process as part of the APLIS
    • Features of a good DMS include the following:
      • Intuitive surface requiring minimal training
      • Straightforward file structure that is easy to access
      • Ability to accommodate AP naming procedure / conventions
      • Accessible across different platforms and locations
      • Collaborative work on same documents by multiple employees at the same time
      • Easy to integrate with the APLIS software
      • Compliance configurations compatible with laboratory policies
      • Enough current and scalable storage space
      • In solution chat and email notifications
      • Security against cyber threats
      • Archiving abilities to enable prolonged storage of documents
      • Customer support
    • Examples of free DMS
      • Google Drive
      • OpenKM
      • Dropbox basic
      • Mayan EDMS
      • Machine installed
    • Examples of paid DMS solutions
      • Microsoft OneDrive
      • Microsoft OneNote
      • OpenKM Professional
      • Ascensio System OnlyOffice
      • DocuWare Cloud
      • Dropbox
      • Box for business
      • SAP DMS
      • Smartsheet
  • APLIS application
    • APLIS application is the layer of APLIS that the end user (e.g., pathologist, technologist) directly interacts with (Adv Anat Pathol 2012;19:81)
    • Regarded as the face of APLIS
    • The user's experience is directly impacted by the user interface design
    • Modern APLIS can present a different user interface for the following purposes:
      • Specimen accessioning
      • Histology (including stain / recut order entry)
      • Transcription
      • Billing
      • Sign out
    • APLIS application layer can be presented to end users in the following ways:
      • Installable desktop applications
        • Simplest and most common mode of APLIS presentation
      • Virtualized application
        • Resides on the server but is presented to the end user like desktop applications
        • More complex than simple downloadable desktop applications
        • Advantages include the following:
          • Client operating system agnostic
          • Protects data from third parties
          • Data storage methods are more secure than traditional desktop or cloud computing methods
      • RIA / web portal
        • Makes use of a set of webpages that are viewable to any modern browser
        • New method in APLIS application layer
        • Precludes the need for additional software installations especially when the end user lacks work machine administrative privileges
        • A major disadvantage, however, is that it is exposed to the internet with consequent security and data ownership issues
      • Text based terminal
        • Primarily of historical interest with minor modern applications in clinical pathology (CP)
Diagrams / tables

Table 1: APLIS components (Adv Anat Pathol 2012;19:81)
Layer Description Examples
APLIS application The software interface to the end user; usually programmed for a specific operating system and almost always programmed for a specific DBMS; has user interfaces for data entry and manipulation Cerner, CoPath, Cerner, PathNet, Orchard, Harvest, LIS, SSC SoftPath
Database management systems A specialized software package for the persistent storage and manipulation of data; currently the vast majority of these use the relational model and implement an SQL interface; in the LIS, high performance is not as important as high reliability, requiring certain tradeoffs to be made Microsoft SQL Server, mySQL, PostgreSQL, Oracle Database, MUMPS
Operating system The fundamental control program through which the end user interacts with a computer; there are different operating systems that are suitable for different niches (e.g., it is far more common for Linux to be the operating system of choice for a server than for a personal computer) Microsoft, Windows, Mac OS X, Linux
Hardware Any physical device that either hosts or interfaces with the APLIS; requires both a hardware and a software interface for the operating system (and APLIS) to function Server computer, client computer, barcode scanner, label printer, slide printer, H&E autostainer
  • This refers to the combined hardware and software setup of devices within the laboratory network
  • APLIS architecture can come in the following architecture setups:
    • Hub and spoke mainframe architecture
      • This method involves the central processing and storage of data at a mainframe computer with the display of information on peripheral terminals that lack processing capabilities; network is centered on a central mainframe computer that is cheaper and easier to secure and maintain
      • A major disadvantage is that a security breach or technical fault in the mainframe computer may negatively affect the whole network (Am J Clin Pathol 1996;105:S25)
    • Client server architecture
      • At present, it is the dominant architecture used
      • End users interact with smart computers that run the APLIS application layer as standalone programs
      • These programs interface over the network with the servers on which the DBMS resides
      • Advantages of this architecture include the following:
        • Uses the computational powers of modern day desktop computers
        • Centralized data management and manipulation
        • Can operate temporarily when the servers go down
      • Disadvantages are as follows:
        • Increased complexity of design
        • Heftier network resources are needed
        • High overhead maintenance cost
        • Excessive cost of security maintenance across different systems (Adv Anat Pathol 2012;19:81)

          APLIS hardware components

    • Thin client architecture
    • Web based (cloud) LIS architecture
      • Enables a laboratory to use web delivery portals provided by LIS vendors
      • Has the advantage of lower installation and maintenance costs
      • A major disadvantage is security and customization problems due to data storage on off site servers (Adv Anat Pathol 2012;19:81)
Diagnostic applications in an AP laboratory workflow
  • The functionality of an APLIS in an AP laboratory can be divided into the following 3 phases:
    • Preanalytical phase
      • APLIS data entry is still largely manual and dependent on paper for the following reasons:
        • APLIS lacks specific dictionary driven texts
        • AP orders require more information compared with CP orders
        • A single AP order may encompass several parts from several organs
        • AP specimen collection is inherently driven and may sometimes lead to accession numbers with no specimen
      • The first interaction of APLIS with a specimen is usually at the time of its receipt at the AP laboratory
      • Specimen is normally followed with a printed requisition
      • Human labor is required to accession the cases on reception
      • After accessioning the specimens, APLIS is used to assign them unique accession numbers
      • Related information from the requisition is entered into the APLIS
      • In multipart cases, each part is entered and documented separately
      • APLIS makes use of data fields to enter specimen information such as those below:
        • Part type data field
          • This is used for specimen types that have been built into the APLIS part type dictionary
          • For these specimen types, information cannot be entered into the APLIS as free text
          • The part type field can also trigger other field types, such as:
            • Fee codes
            • Histology protocols (e.g., H&E X3, immunohistochemical stain for H. pylori)
        • Part description field type
          • This part is most often entered in free text
          • Comprises the descriptive information about the specimen that was provided in the requisition (e.g., LUL 2 cm mass lung biopsy)
          • Provides relevant information to the pathologist interpreting the case
      • The following patient information can be entered into the APLIS:
        • Location of specimen procurement
        • Patient demographics
        • Billing, etc.
      • Patient information is entered electronically using an ADT feed transmitted from the HIS
      • Patient information can also be manually entered by an accessioner, though this method is prone to errors
      • At the end of a specimen entry into the APLIS, the case is updated to accessioned, effectively ending the preanalytical phase (Adv Anat Pathol 2012;19:81)
    • Analytical phase
      • The first part of this phase is referred to as grossing and is comprised of the following:
        • Description of the gross appearance of specimens
        • Dissection of the specimen
        • Selection of individual tissue sections
        • Designation of tissue sections for microscopic examinations
      • Gross descriptions are done in free text
      • Text templates for commonly processed specimen types exist (e.g., colon polyp biopsies)
      • Speech to text recognition software have recorded successes at this phase
      • A gross specimen report is generated at the end of grossing, which contains the following:
        • Description of the specimen
        • How it was dissected
        • What was seen macroscopically upon dissection
        • Alphanumerical list (key) designating what tissue went into each cassette
      • Cassette engraves that are interfaced with APLIS do not provide enough information on the kind of tissues that went into each cassette at the end of grossing
      • As a result, tissue cassette designations must be entered into the APLIS manually
      • Gross specimen digital images obtained during grossing have APLIS modules capable of accommodating and managing them

        APLIS digital image

      • This phase also makes use of the part type dictionary for cut sections and stains during slide preparations
      • Specimen tracking, barcoding and radiofrequency identification (RFID) technology can be used to update specimen status and location
      • Autogeneration of barcodes and slides labels have also been used by some LIS at histotechnologist stations during microtomy to reduce case misidentification and improve efficiency
      • Completed slides are paired with an autogenerated working draft (case assembly)
      • The case assembly above is usually templated in an LIS dictionary and it includes:
        • Patients’ demographics
        • Relevant clinical history
        • Gross description of the specimen
        • Interoperative consultation diagnosis (e.g., frozen sections)
        • Patients' past AP reports
      • Final pathologic diagnosis is mainly done with free text
        • Sometimes involves the transcription of a pathologist's dictation
        • Predefined templates or quick text can be used for frequent diagnoses (e.g., tubular adenoma)
        • Speech to text conversion by voice recognition software can be used as well
      • After entry of a final diagnosis, the case is marked as final on the APLIS and placed on the pathologist's worklist for final edits and electronic sign out
        • Billing and diagnostic codes are generated automatically at this stage
      • Final report is then transmitted into a downstream system, such as the clinician's EMR
      • There is a push for increased adoption of structured synoptic reports and checklists
        • This is an improvement over the use of free text for data storage

          Synoptic pathology report

          Synoptic worksheet

      • Advantages of synoptic reports / checklists:
        • Make reporting more efficient
        • Standardize reporting among surgical pathologists
        • Contain all the data elements required on a diagnostic checklist (e.g., the CAP cancer checklist) (Adv Anat Pathol 2012;19:81)
    • Postanalytical phase
      • The following methods can be used to transmit pathology reports to clinicians:
        • HL7 messaging system is used to send patients' reports to a hospital's EMR for easy access by clinicians in that hospital
        • Automatic faxing is used to send reports to clinicians in an external hospital
        • Online portals can also be used to store patients' reports and clinicians who need the reports are given access to the portal
      • APLIS also allows amendments and addendums to be added to final reports (Adv Anat Pathol 2012;19:81)
Diagnostic applications in digital imaging
  • Recent advances in WSI have raised the possibility of an all digital AP workflow (J Digit Imaging 2020;33:1034)
  • APLIS can be integrated with digital pathology in the following ways:
    • APLIS as an image management system
      • Many AP practices now exclusively use digital cameras to take pictures of gross and microscopic specimens
      • APLIS can be applied to the following digital imaging processing stages:
        • Acquisition
          • Refers to the process of creating digital images
          • End users usually import images into the LIS using separate applications
        • Storage
          • Digital images can be stored on the LIS using the 2 approaches below:
            • Integral image management
              • In this module, the image is stored and managed in the database of the LIS

                APLIS digital image

              • Advantages:
                • Images can be kept in the gallery for internal use (e.g., for documentation purposes)
                • Images can be copied into final reports
                • Contains the details of the image, such as dates, locations and users who took the pictures
              • Disadvantages:
                • Image editing is restricted to what the LIS supports
                • End users find it difficult to access the raw image data
                • If the LIS fails, the digital images in system are lost as well
                • File format of image storage hinders interoperability
            • Separate (modular) image management
              • Makes use of a different application that automatically feeds images into the LIS

                APLIS image storage modules

              • This module can do the same work as the integral module above using different means
              • Advantage: end users have the flexibility of using image editing software on the image
              • Disadvantages: increases overhead cost; this module may not be compatible with certain LIS
          • Manipulation
            • Refers to the annotation or transformation of images using image editing software (e.g., insertion of measurements and captions)
          • Image sharing
            • Image sharing can be done in the following ways:
              • Integration into final reports
              • For use in consultations
              • As adjuncts to tumor board presentations
            • Advantage: image sharing facilitates teaching and communication to patients and clinicians
            • Disadvantage: legal liability for embedding images in pathology reports is not well understood (J Am Acad Dermatol 2006;54:353)
    • APLIS applications in digital pathology sign outs
      • There is a need for an APLIS WSI interface that fulfills the following needs of an anatomic pathologist:
        • Relevant case data, including intraoperative notes
        • Old surgical pathology cases from the same patient
        • Patients' clinical notes
      • Most current APLIS WSI interfaces rely on at least 2 monitors to meet the needs listed above:
        • 1 monitor to display the WSI
        • The other monitor to display the case and clinical data
Diagnostic applications to cytopathology
  • APLIS holds unique opportunities for cytopathology as a whole (Cytojournal 2008;5:16)
  • Cytopathology workflow differs from surgical pathology in that slides prepared for pathologists are first screened by cytotechnologists
  • Thus, some APLIS allow separate fields for the impressions of the cytotechnologist and the final diagnosis
  • APLIS design for cytopathology must integrate the following:
    • Whether the obtained specimen is adequate (satisfactory or unsatisfactory)
    • A primary interpretation (negative, atypical, suspicious, positive)
    • Final diagnosis
  • APLIS used for gynecologic and thyroid cytopathology must integrate dictionaries codified in the Bethesda system terminology
  • The use of APLIS in creating standardized data allows for reflex testing (e.g., ASCUS for a Pap test followed by a reflex high risk HPV testing) (Clin Lab Med 2007;27:823)
  • APLIS must also take into consideration the cap on the maximum number of slides allowed for manual screening per 8 hour periods by a cytotechnologist
  • It must also consider the rescreening rates of negative Pap smears allowed for cytotechnologists based on their years of experience
  • It must ensure that all slide rescreening in a practice is done appropriately (Cytojournal 2008;5:16)
  • LIS could also be used to flag high risk cases using the following markers:
    • Previous history
    • Current history of abnormal signs and symptoms
    • Pathologic findings
  • The method above can improve the detection of Pap smear cases diagnosed as LSIL in the previous year
  • These APLIS cytopathology measures will improve patient care and turnaround time (Cytojournal 2008;5:16, Adv Anat Pathol 2012;19:81)
Summary of applications
  • APLIS provides a reliable information structure in modern anatomic pathology laboratories today by:
    • Registering specimens
    • Recording gross and microscopic findings
    • Regulating laboratory workflow
    • Formulating and signing out reports
    • Disseminating reports to intended recipients across the whole health system
    • Supporting quality assurance measures (Adv Anat Pathol 2012;19:81)
  • When integrated with digital pathology systems (DPS), APLIS improves AP diagnosis as follows:
    • Improves the efficiency of digital sign out for primary diagnosis
    • Makes teleconsultation more practical and efficient
    • Streamlines the digital sign out workflow

      Integrated APLIS (CoPath Plus) and DPI (Omnyx IDP)

      APLIS DPI interface

Applications to data warehousing and data mining
  • Data mining refers to the use of computers to analyze substantial amounts of data to identify meaningful and statistically significant patterns (Adv Anat Pathol 2012;19:81)
  • Mining of large scale clinical trials, for instance, provides new directions for research and health policies
  • In APLIS, data mining is used for quality assurance (QA) and tissue bank support
  • Examples of APLIS application in data mining includes the following:
    • How long a pathology department takes on average to sign out a breast biopsy
    • Flagging unusual cases for review
    • Running analysis on the number of bankable tumors banked over a given period
    • Specimen rejection frequency by a clinician's office
    • Periodic reports that identify trends associated with any clinician's office
  • Challenges to APLIS based data mining in AP include:
    • Diagnostic terminology changes over time
    • Almost all AP gross and final reports are handled as free text
  • Challenges to APLIS data mining can be gradually overcome by the increased adoption of synoptic grossing and reporting (Am J Clin Pathol 2009;132:521, Chen: Medical Informatics - Knowledge Management and Data Mining in Biomedicine, 1st Edition, 2005)
  • College of American Pathologists currently advocates for increased use of discrete data capture via synoptic reporting (Dovepress: Current Status of Discrete Data Capture in Synoptic Surgical Pathology and Cancer Reporting [Accessed 10 February 2023])
    • The goal of such moves is to significantly improve the quality of pathology reports used for quality assurance, data mining and other related functions
  • Built in software features such as spell check and automated comments can be used to improve LIS data mining capabilities (Adv Anat Pathol 2012;19:81)

What is an LIS (laboratory information system) and how does it work?

Laboratory management information system

Board review style question #1
Which of the following presents the most significant challenge to the use of anatomic pathology laboratory information systems (APLIS) for data mining purposes?

  1. Limited access to electronic medical record (EMR) and hospital information systems (HIS) by APLIS software
  2. Poor APLIS whole slide imaging (WSI) computer interface
  3. The complexity of the data to be mined
  4. The prevalent reporting of AP grossing and final diagnostic reports using free text style
Board review style answer #1
D. The prevalent reporting of AP grossing and final diagnostic reports using free text style. Almost all AP gross and final reports are handled as free text, constituting a major barrier to APLIS based data mining (Adv Anat Pathol 2012;19:81).

Comment Here

Reference: APLIS
Board review style question #2

What is the best way to improve the quality and standard of diagnostic reporting in anatomic pathology practices that make use of anatomic pathology laboratory information systems (APLIS) applications?

  1. Increased adoption of synoptic grossing and reporting worksheets for surgical pathology specimens
  2. SQL integration into the APLIS software
  3. Upgrade of the operating systems on which APLIS applications run
  4. Use of the relational model in the database management systems of APLIS
Board review style answer #2
A. Increased adoption of synoptic grossing and reporting worksheets for surgical pathology specimens. Challenges to APLIS data mining can be gradually overcome by the increased adoption of synoptic grossing and reporting. The use of synoptic grossing and diagnostic worksheets for reporting AP specimens will also improve the quality of pathology reports overall by ensuring that relevant diagnostic components are not overlooked in the final report. In addition, it will enable the laboratory to comply with nationally and internationally accepted guidelines in pathology for diagnostic tissue reporting (Am J Clin Pathol 2009;132:521, Chen: Medical Informatics - Knowledge Management and Data Mining in Biomedicine, 1st Edition, 2005).

Comment Here

Reference: APLIS
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