How to Choose an Anatomic Pathology Laboratory Information System (LIS)


In a previous article we commented about the definition of an APLIS.   In this article, we’ll explore at least one way in which an organization can choose an APLIS from amongst all the choices present.

If you are looking for an APLIS, you have a lot of choices and a lot of material that can potentially help you make those choices.   In particular, there is a yearly listing of APLIS vendors presented in the publication, CAP TODAY.   Research the internet a little more and you will find an LIS Functionality Assessment Toolkit that has a section devoted specifically to Anatomic Pathology.   Both of these resources provide good starting points for

What systems are available?

What types of questions should I be asking?

 However, before plunging into the details of an RFP or compiling a list of specific questions, it would be wise to consider the overall objectives of your search.   What specifically do you want to get out of your APLIS?  Consider the importance of this question.

  • An APLIS is a major expenditure in terms of time, money, and effort.
  • It is a decision that you will live with for more than likely 10+ years.
  • It is a decision that you will interact with on each and every case, multiple times an hour, a day, a month, a year.    There may be nothing else that you interact more with than your APLIS, except perhaps the specimen material itself.


Have we got your attention?   Yes, this is important!


To choose a system that won’t drive you crazy on a daily basis, or worst yet, bankrupt your organization, start with a definition of your objective.   Start at a global level and then drill down to the details.   For instance, are you looking for a

1.        Reporting system?

2.        Tracking system?

3.        Dashboard system?

4.        Metrics system?

5.        Interface engine?

6.        Or perhaps it’s all of the above or something else?

After you have your global concepts enumerated, use the toolkit mentioned previously to help define what these concepts really mean to your organization.  Consider not only current problematic workflow areas, but make sure to consider workflow aspects that work well.   Surely, you want your new APLIS to address your current problems, but you also do not want to go backwards in those areas that currently function well.   While you are reviewing the literature pay attention to those workflow aspects that are relevant to your own organization and do not be afraid to disregard issues that are important to other organizations.   For instance, if your environment only requires an interface to one or two outside organizations, perhaps an interface engine is not required.  Interface engines are useful when interfacing many outside clients, but can be overkill when, for instance, you are only sending results back to 2 outside providers.

Consider not only IF a vendor provides a sought after functionality, but pay close attention to HOW the vendor provides specific functional capability.   If one vendor’s product takes 10 steps to accession a case and another vendor takes 20 steps to accession the same case, you can only imagine the time your laboratory will lose when you multiply that by thousands of cases a year.  This point cannot be emphasized enough.  Workflow, keystrokes, and number of screens have an impact that is multiplied by the thousands.

Software functionality is extremely important.   However, equally important is the type of vendor chosen and the type of relationship between the laboratory and the APLIS vendor.   The type of vendor a laboratory chooses can have more of a future impact than the software functionality. This aspect of an APLIS purchase is often overlooked or perhaps, glossed over.  As you are analyzing a particular vendor’s offering, pay particular attention to the vendor itself.  Think about it this way.  Once you’ve purchased the software,

o   How do you get the software fixed?

o   How do you get the software updated?

o   How do you get the software changed JUST FOR YOUR ENVIRONMENT?

The type of vendor you select and the objectives behind your APLIS purchase all combine to address the issue of the vendor/client relationship.  For instance, if you’re buying an APLIS just to meet regulatory compliance, then your organization will probably not require a vendor to change their software just for your specific needs.   On the other hand, if your organization views the APLIS as an absolutely critical component of daily operations and that it is something that you’ve purchased to give the organization a strategic edge against the competition, then you’re going to want a vendor that is responsive and receptive to your needs.   APLIS vendors are very different.   Generally, larger vendors emphasize stability while smaller vendors emphasize flexibility and engagement.  This is not an absolute rule, but appears to be a general trend.

Choosing an APLIS is an expensive and important decision.   It is a decision that you will interact with many, many times over many years.   To increase your odds of selecting the right system, define your objectives on a global level and then narrow your focus as you define your parameters.   Know what you want your APLIS to do for you and pay attention to how a vendor’s offering satisfies your needs.   Do not be myopic!   Pay attention to the relationship and the type of vendor you are signing up with.   Unlike a car purchase, you generally cannot get support from anyone else except the original APLIS vendor.  Your selection of a system and a vendor will affect your laboratory for years to come…

and may just determine if you’re in business in a few years….

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HR 4302, Meaningful Use 2, and ICD10

The passage and presidential signature of HR 4302, “Protecting Access Medicare Act of 2014” extended a number of SGR (Sustainable Growth Rate) rules beneficial for providers.  Most notable are the delay in the 24% cut to Medicare reimbursements (reduced to 0.5% for the remainder 2014 and 0% the first quarter of 2015), Medicare volume hospital payments, and Medicare SNP (Special Needs Plans) among others.  Included in HR 4302 was the delay of the use of ICD10 coding in CMS transactions by an additional year to 01 Oct 2015.  Nothing in HR 4302 changes or delays Meaningful Use!


Meaningful Use deadlines for stage 1 and stage 2 remain in effect.  For EP’s (both providers and hospitals) the last MU1 (MU stage 1) attestation deadline for 2013 incentive and quality payments for 2013 was 28 Feb 2014.  To avoid the first CMS 1% penalty for stage 1 your practice must attest no later the third quarter of 2014.  MU2 (MU stage 2) deadlines for reporting attestation to reduce Medicare penalties occur on 01 April 2014, 01 July 2014, and 01 October 2014.  The passage of HR 4302 and the ICD10 delay does not affect any MU attestation deadline.  Any hospital or practice that provides care to Medicare patients and chooses does not participate in MU or fails to achieve MU target thresholds will have reductions in Medicare reimbursements rates as described by the ARRA which are approximately 1.0% each year.


Thresholds targets for attestation declared for MU stage 1 have increased at MU stage 2.  A sampling of selected quantitate measures for EP (Eligible Professionals) are presented below to illustrate these trends:


Core Objective (EP’s Hospitals & Practices) Stage 1 Stage 2
CPOE >30% of all patients withmedication orders >60% medication orders>30% LAB orders>30% RAD orders
e-Rx >40% >50%
Demographics >50% >80%
Vital Signs >50% >80%
Smoking Status >50% >80%
Incorporate LAB >40% >55%
Clinical Summary >50% within 3 business days >50% within 1 day
Provide Patient view, download, & transmit
Protect PHI on CEHRT certified applications Conduct security reviews Conduct security reviewsEncrypt PHI in storageInternal audits


System implementers have daunting challenges first established in MU1 that continue under CHERT into stage 2.  Problem lists must utilize SNOMED CT rather instead of ICD code sets.  All CQM’s (Clinical Quality Measures) also require use SNOMED CT.  Under CHERT 2014 rules the use of HL7 2.5.1 or CDA R2 messaging standards and the vocabularies of SNOMED CT, ICD-10, and LOINC 2.38 are mandated.  ONC has sponsored several S&I LAB initiatives that are currently developing the required HL7 IG’s (Implementation Guides) for these technical efforts.


CMS regulations do allow for hardships exemptions from payment reimbursements adjustments.  The major categories for filing exemption are: (1) Lack of Infrastructure, (2) Unforeseen or Uncontrollable Circumstances, and (3) 2014 EHR Vendor Issues.  These exemptions must be filed annually and cannot be sustained beyond 5 years.  The documents you need to file a Hardship Exemption are the CMS TipSheet and the Hardship Exemptions Form which can be found on the CMS web site at


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What Is an Anatomic Pathology Laboratory Information System (LIS)?

Where are my slides?
How could we have mixed up the slides for two different patients?
Why are my slides difficult to read?
We lost a slide!!!

These are the types of issues an Anatomic Pathology Laboratory Information System (APLIS) should help your laboratory to address. As its core objective, an APLIS should help the laboratory to record, track, and distribute the results of the efforts of a myriad of individuals working together to produce an accurate and detailed diagnosis from the samples provided to the laboratory.

The pathologist’s position in this collective effort lies at the end of the chain, and there are quite a few things that can go wrong before the pathologist views the initial case slide.

Consider a breast case where multiple samples can each yield multiple blocks, which in turn can each yield multiple slides. A patient sample that started out as two or three sample containers can result in thirty or forty related material samples. Now, multiply this by tens or hundreds of cases a day. Take into consideration that this material is handled by several different people and instruments, and it becomes quite easy to see why the typical Anatomic Pathology Laboratory is at a higher risk of error than other areas.

An APLIS should address these concerns by allowing all pertinent information to be entered into a system whereby this information is easily retrievable by the pathologist or anyone else connected to the workflow process.

What does this mean?

Consider the information needs of each person who has anything to do with a patient sample, be it the order entry clerk, the PA, the histotechnologist, the secretary, or the pathologist. What information do they need quickly and accurately in order to do their job? For instance:

  • What special instructions did the requesting clinician provide?
    • Call the results?
    • Process the sample stat?
    • Special instructions?
  • When the sample was grossed, were there particular observations to be noted? Are these recorded and easily viewable to the pathologist?
  • At embedding, are there any special embedding instructions?
  • As the histotechnologist prepares the various slides, can they view the pathologist’s instructions?
    • Are the instructions easily viewable?
    • Can the tech enter comments that will be easily viewable by the pathologist or anyone else?
  • As slides are distributed, is it easy to determine that all slides are at hand?
  • When the pathologist receives a tray of slides:
    • Is it easy to determine that all slides for a case have been received?
    • Is patient history easily and accurately viewable?
    • Can additional stains be ordered easily?

This is just a sample of the types of issues an APLIS should address. Consider your workflow and consider the information requirements and each step of the process. Then, work backwards and ensure that each piece of information is available to everyone who needs that information.

Software functionality is certainly a large part of the equation when one considers an APLIS. However, it is far from the only consideration. Perhaps the most salient point is that you will get out of an APLIS exactly what you put into it. If you believe an APLIS is simply a necessary evil, then that’s what you will get out of it. If you look at your APLIS as a tool that will pay dividends over the long run, then if you work with the software and if you work with the vendor you will be the recipient of higher quality and more accurate workflow day in and day out.

In future articles, we will discuss how to choose an APLIS and how to implement and manage an APLIS.

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Tracking Systems

A tracking system is not just simply the printing of bar-codes on specimen, blocks, and slides.  This is only the beginning.

Bar-coding the different materials found in the histology and cytology laboratories, for that matter, simply provide a quick and accurate mechanism to uniquely identify these materials.  The real ‘magic’ is how various computer systems use this capability.

PathView believes that tracking system functionality is such a fundamental requirement that we have built an entire Laboratory Information System (LIS) around this functionality.  Our LIS cannot be purchased without tracking.  It’s not the 99.9% of specimen, slides or blocks that are routinely processed that create issues in the laboratory.  It’s those blocks and slides that are ‘lost’ or misplaced or misidentified which create the errors and road blocks in your laboratory.  Consider that on any given breast specimen, you may have 10 to 15 blocks which may yield another 1 or 2 slides and you suddenly find that on 1 case you can have 30 different materials to label, track, and analyze.  Having an LIS that incorporates a tracking system at it’s core has multiple benefits:

  • Tracking happens behind the scenes so there are no extra steps to the daily workflow.
  • Absolutely everything that occurs to any piece of material that is associated with a case can be displayed in a single screen.
  • At every step of processing, no matter what the material type, an automatic inquiry displays absolutely all facets of the case to the person working with the material.
  • Quality control commentary and actionable alerts can be entered and displayed to let everyone in the laboratory know what is going on with the case.
  • Management reports provide detailed statistics to the laboratory manager.   A limitless number of reports can be customized by the manager to analyze any specific step of the workflow process.
  • Tracking steps are user configurable and may be temporary or permanent in nature.  New workflow steps may be trialed and analyzed for success.

If you’re organization is not in a position to consider a new LIS, consider the following issues which may affect your middle-ware selection:

A tracking system may cost as much as $300,000.  The typical PathView software cost  is much, much less.

Enterprise Wide Tracking
In multi-site organizations or organizations with many private clients, consider that a middle-ware tracking system simply tracks material AFTER it has reached the laboratory.  Many errors occur before the specimen reach the laboratory and having two separate systems track the various workflow steps can cause multiple difficulties.

Data Transfer to the middle-ware product
How will information get into the middle-ware tracking system?  Will it have to be manually accessioned/entered or will there be an interface?  If there will be an interface, there may be an interface cost for either direction and from either or both vendors (current LIS and middle-ware vendor)

Data Transfer from the middle-ware product
How will information get OUT of the middle-ware product or put another way, does the pathologist or secretary need to see information gathered/stored by the tracking system?  It’s always nice to see the complete picture in a single presentation so keep this issue in mind.

System Maintenance
Who is going to configure, manage and maintain the tracking system?  This is going to be an entirely separate computer system in your lab.  Will your IT department support it, maintain it, administer it, etc.  Who will understand and set up the files, etc.?  What is the maintenance cost of the tracking system from the middle-ware vendor?

Pending Displays
Are comprehensive pending displays available and easily selectable?

Management Reports
Are sufficient reports available?  Are reports customizable so that new trends and trials may be analyzed?

Many laboratories are now scanning copies of requisitions into their LIS.  Will these be available in the tracking system?  Will the patient history be available in the tracking system?  Is this required?

Are PCs required at every cutting and embedding station?  This will add to the system cost and may present space challenges.

Instrument Compatibility
Does the middle-ware/tracking vendor selection restrict your purchase of future instrumentation?  Some vendor’s tracking systems only work with their own instrumentation.

In summary, there are two general approaches to tracking material in the histology and cytology laboratories.  We clearly believe that the best choice is to track material in the AP/Cytology LIS.   However, in situations, where this is not practical, middle-ware vendors are an alternative.  In the latter approach appropriate attention must be given to the issues inherent in that solution.
PathView Systems, Ltd.

© 2002-2011 PathView Systems, Ltd.  All Rights Reserved.

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Benefits of a good LIS

Tracking systems are just one of the many tools that should be at your disposal to help ensure that your laboratory generates a quality product. If case material is lost somewhere in the workflow and no quality alerts are triggered, that’s obviously not a good thing.

Quality Assurance and Quality Control needs to be an integral part of every step in the process. It’s a mindset that every team member must have day in and day out. I doubt that many of you would argue with the premise. In the real world, however, it’s awfully hard to keep quality issues in mind when your work is further and further compromised because of reduced staffing, daily crises, or simply overwhelming volume.

This is where your LIS should come to the rescue. Your LIS should help you prevent ‘dumb’ mistakes. It should help you ‘see’ problems as they occur, and it should help you analyze your workflow as a whole rather than require a conglomeration of multiple manual steps.

Here are some examples:

  • Case entry is where the pre-analytical phase meets up with the analytical aspect of the process. Does your LIS allow you to see pending interface orders and act on them prior to case creation? Can your clerk log labeling and other collection errors without moving to separate screens? Remember that this is a very high volume step of the process. If you ask your clerk to log errors in separate screens, the likelihood of that occurring is less likely than if the tracking of issues is part of the accessioning screen itself.
  • During grossing, embedding, cutting, and slide distribution all pertinent information about the case and any quality alerts should be automatically presented. These tend to be production level steps of an assembly process. Please don’t ask your team members to click on inquiry screens or navigate multiple screens at four in the morning when there are hundreds of cassettes to be embedded and even more slides to cut. Your LIS should allow each member to enter quality comments AND know that this information will be not just available but automatically presented to everyone involved with the case.
  • Entry of results, be they synoptic surgical case type, or Bethesda pap results should encompass a wide array of quality algorithms, both as results are entered and taken as a departmental whole. Are there departmental alerts emailed to the chief pathologist? Are cases selected for random QC validation as results are signed out? Does your LIS allow previous results to be modified after they are selected for quality review?
  • The LIS should constantly be gathering data in the background. Taken as a whole, management should be able to use this data to identify and resolve issues with the laboratory workflow. There are a limited number of systems that do this well. Can your system identify and analyze process steps on a temporary vs. permanent basis? For instance, few laboratories go through the trouble of scanning cassette barcodes as cassettes are placed into and taken out of processors. However, there are times when changes in workflow cause issues in this area. Your LIS should be flexible enough to allow you to track these workflow steps for a period of time until remedial actions resolve issues, and easily disable the additional steps when appropriate.

The LIS should help your department generate a quality product. It should do what computers do best; ensure that each specimen, block, and slide is handled in a manner that assures the most accurate analysis, no matter what the volume, staffing, or phase of the moon.

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