Talk:APW-EDM White Paper

Discussion Page for APW-EDM White Paper

NOTE FROM NCJ: Per Gunter's suggestion, I made the discussion page, and I'm moving a lot of my comments/questions that I had written in text over to here. Hopefully that will make the main page for drafting the white paper less messy and more readable. -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

NOTE2 FROM NCJ: I wanted to add discussion sections for issues originally referenced in word document drafts of the white paper, so I've added those to this page after the discussion of use cases. That includes sections on describing specimen processing, imaging process ordering, tracking, and results, digital image management, and image display. Furthermore, I don't think we've been recently discussing actors and transactions, so I've added those as well. Since I did these things electively (not discussed in the last meeting), I thought it best if I put those down on the discussion section rather than the main page, in case the group things I'm veering off course... -Nicholas C. Jones (talk) 08:28, 19 May 2018 (CDT)

Discussion: Use Case #1: Image Slides for Secondary Review / Consultation

Regarding 1c: NOTE FROM NCJ: Dr. Dash: can you verify that we should separate this out from 1b or should we put it as a sub-category under 1b, since the physician here is going to get pt consent for the consultation anyways? In my experience though, these are of noteworthy difference both in clinical processes and in likelihood of impact /avg value from 1b. -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

Regarding time frames for returning glass slides: (NOTE FROM NCJ: In the US, the norm is 30 days, though I believe this is a norm rather than a law. Are there differences in practice in Europe and other areas of the world?) -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

Regarding 1e: NOTE FROM NCJ: I am not familiar enough with these processes to go into depth here. It's even worth questioning that we want this in the profile, as it's only semi-clinical. But I think there's at least benefit in mentioning that this is something to consider for system and workflow design so the vendors are at least aware of this as a different use case. What do the rest of the white paper team think? -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

NOTE FROM NCJ: Hopefully between the contexts listed above, the consultation contexts ppt & discussion in the teleconference, and future discussion, we can all get to the same page on why these contexts have significant differences in workflow. The big question to me is do we want to make 1 big decision tree profile for all consultation, different trees for different contexts, or do the other authors have other suggestions? I must note that this is a big area where there is a gap in functionality for many vendor products, because these nuances have not been explained in white paper form previously. So while we might recoil from the complexity here, I think this is a key area of value of the white paper, but I am open to constructive criticism here. -Nicholas C. Jones (talk) 15:12, 13 March 2018 (CDT)

Note from NCJ - I moved most of the text from the white paper area here. -Nicholas C. Jones (talk) 07:58, 4 April 2018 (CDT)

• 1.a. Pathologist requested consults, pre-primary diagnosis.
  • 1.a.1. Intrainstitutional: The pathologist is requesting a second opinion (through digital review) to another pathologist at their institution, either at the same site or another site in their network. In the case where the pathologist was already viewing the slides digitally (primary diagnosis), this would likely be in the same system (i.e. uses synchronous or asynchronous consultation functions within their IMS/PACS). This is likely due to the case being challenging, or otherwise meriting the review of a sub-specialist (or different kind of subspecialist, such as a gyn-specialist requesting the opinion of a dermatopathologist's consultation).
    • Note that this may or may not trigger requests for scans, would not trigger billing for the patient, but may trigger records or documents internal to that organization for tracking consultation between pathologists within the organization.
    • Note that due to the internal nature, it can be assumed the consultant will have access to all electronic documentation (EHR, APLIS, etc.), but that there are likely to be either text based messages and annotations (for asynchronous consultation) and/or verbal communication between requester and consultant in the case of synchronous consultation.
    • Much of the value of this process centers around efficiency (compared to glass slide processes) is in limiting "phone or email tag" issues, maximizing communication ("this ROI is what worries me"), and generally improving organization and documentation of the process.
  • 1.a.2. Interinstitutional: The requester pathologist is requesting consultation from an outside hospital, usually due to the challenge of the case or the need for an external subspecialist.
    • Slides may need to be scanned if the requester was using the microscope. The requester pathologists may only request a subset of the slides to be scanned (i.e. if 9 slides are normal, and 2 are questionable, they may scan and send just the 2 questionable slides to the consultant.) Note that in this context, the scanning processes will likely be considered high priority or rush requests; systems should allow for differences in priority of scan requests.
    • The request to the consultant will be coupled with consultant's summary of the patient's clinical history, notes and questions (i.e. "is this a microfocus of carcinoma?" or "my differential is diagnosis A vs diagnosis B.") along with printed or saved documentation (i.e. preliminary report including items like frozen section or rapid fine needle aspiration interpretations, reports from surgeons or radiology imaging processes, other images from AP processes such as gross images, IF, EM, etc.) and possibly blocks. Inclusion of profiles like APSR here will be highly beneficial, especially if APSR profiles support itemizing both all assets that exist on a case as well as what was sent for consultation.
    • Note that the consulting institution will need to match images to clinical history and documentation. The consulting institution may also have quality control procedures to check image quality, and may need to troubleshoot the process by asking for rescans or other clinical information.
    • There are potentially significant differences in process here based on how image distribution and viewing are intended to function. This may involve uploading WSIs and other data to a thin client host, uploading data to a repository for download to the consultant group, or sending disks (i.e. flash drives or DVDs) with the data.
    • Much of the value proposition in this process revolves around reducing turn-around-time of processes versus mailing glass slides, further coordinating the consultation process (which requires some collaboration between the requesting site and consultant site), and improving on the consultation product to the requester (i.e. requester gets the consultant's report in the end, but can also see annotations or other notes to see in more detail why the consultant interpreted the case in such a way). These value propositions also merit noting that sending physical media can potentially be viewed as "the worst of both worlds" if they require both imaging processes and still have the long shipping time related issues and risks.
• 1.b. Patient requested second opinion, post-primary diagnosis.
  • These contexts can be generally assumed to be going to a different institution. While there may be less pressure on the original institution for timeliness, the patient may be waiting on making a treatment decision based on the second opinion, so process turn-around-time is still very important. But because the patient is likely requesting the review sent to a specific institution or other pathologist, it should not be assumed that there is a functional telepathology pipeline between the two institutions.
  • If there are no specific instructions accompanying the request (other than send this case X to institution/pathologist Y for second opinion), the onus is on the institution sending the material to gather materials (documents, images, scanned slides) for send out. The original hospital may wish to image some or all cases for such send-outs either to archive such materials (to mitigate risk of slides being damaged or lost in transit by having digital copies), or to prevent such risks by sending WSIs instead. There may be less benefit of this process context to the consultant pathologist or institution (other than mitigating risk of damage or loss of glass slides) unless workflows are set up to improve turn-around-time, organization of data, or some other benefit to the consultants. It is important to consider the consultants as stakeholders in these processes as well.
    • Again, exact processes will vary based on image distribution (i.e. whether WSIs and other clinical data are made available for download, sent via physical media such as DVDs, or other methods).
• 1.c. Physician requested second opinion, post-primary diagnosis
  • These requests usually come from (non-pathologist) physicians prior to making treatment decisions with the patient. Some physicians (such as oncologists) do this routinely for all new patients, as even a low probability of changing the diagnosis can yield huge value for the patient by preventing unnecessary or inappropriate treatments.
  • It is common for the physician to request the second opinion be sent to the their institution (especially common in academic medical centers, as the clinician may interact with the patient on tumor boards or future biopsies or excisions), or have preferred consultants outside their institution (more common in smaller institutions). Retaining images of prior slides are of significant clinical benefit to pathologists that will review future biopsies or excisions for the patient, as glass slides are generally sent back to the original institution within a specified timeframe.
• 1.d. Second-opinion broker requests, post-primary diagnosis.
  • These are a hybridization of 1b and 1c. Patients may request the services of second opinion brokers to organize consultation on all of their case, including pathology but also radiology, oncology, and other areas. The second opinion brokers provide case management services, and may delegate different aspects of the overall consultation to different groups.
  • Differences in the organization of these processes merit their mention here, as the group managing the consultation is external both to the original diagnosing institution and the consultant pathologists. Workflows and data pipelines may either go through the second opinion broker's systems or otherwise need to be coordinated with the second opinion broker organization who act as proxies on behalf of the patient.
• 1.e. Legal cases, post-primary diagnosis.
  • In these cases, imaging may occur to archive the case prior to glass slide send-out for consultation, or to send out the images to legal teams which will seek consultants.
  • Workflows for legal cases are significantly different than clinical processes, but may be less urgent (for clinical care purposes) than other contexts discussed above.
• 1.f. Consultation for intraoperative interpretations of frozen section or rapid FNA slides.
  • This should be clearly delineated from use case #11 as those individuals requesting a second opinion. (I believe this is done in at least Canada for neuropathology frozen sections.) Such workflows would need to be very fast (if the patient is under anesthesia, the slide was already made, and a first pathologist already consulted) and thus may require special extra steps like pre-communicating the possibility of a required consultation, bypassing other normal administrative processes to get the images to the consultant immediately, and/or receiving verbal interpretations over the telephone during consultant visualization.

Discussion: Use Case #2: Immunohistochemistry Positive Control Slides

We should return to this when we discuss identification edge cases. These control slides would need to be associated with multiple cases (potentially the case of origin + each other stain on that run of the stainer that the control slide is functioning for).

Discussion: Use Case #3: Managing Digital Assets for Primary Diagnosis

Old text pasted here:

These workflows include use of whole slide images for primary diagnosis. The first workflow described is a general workflow for glass slide production in a surgical pathology laboratory, followed by modification for use in digital pathology for Creating digital copies of all glass slides for primary diagnosis

• Specimen collected and transported
• Specimen gross exam with possible digital imaging and annotation
• Specimen processing
• Glass slides produced as usual
• All glass slides fed into high volume automated digital scanner
• Scanner tags images requiring manual intervention
• Digital images deposited in network share, VNA, or PACS
• Interface message to LIS sent as each barcode read off slide
• Acknowledgment from LIS indicates case is valid and ready for association with digital slide assets
• Additional message sent when slide digitization completed
• Interface message sent every time slide viewed or annotated

To be refined and continued.

Discussion: Use Case #4: Sharing and Cooperating on Gross Examination Images

If anyone is less familiar with the grossing process in general, I thought | this article on gross descriptions and specimen processing for GYN cases and | this e-Manual for grossing might be useful references.

Also I wanted to query the group to see if people thought we should include discussions on structured gross descriptions & section codes. It will be highly desirable to have the APLIS be able to send information to digital pathology systems that include reference to the sectioning information (i.e. that block A4 comes from this area of the original part) for both display purposes and communication. Ideally we want to be able to pass information from viewers (i.e. margin measurement or designation of a slide as representative of the diagnosis) into structured reports, and that can become quick and easy if that is modeled into the processes.

That may/would require gross description & tissue section codes that capture not only the text provided by the individual(s) doing the grossing, but also something like XML in the background to separate which text applies to which blocks such as A2 is from the head of the pancreas.

Does anyone have any thoughts on that or ways to phrase that more concisely? -Nicholas C. Jones (talk) 11:01, 21 April 2018 (CDT)

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On behalf of Laurent Duval : Solution Architect - Roche Tissue Diagnostics :

These gross description & tissue info are already supported in HL7 (at least what we do here in Roche Tissue Diagnostics) : Cassette description, number of fragment per cassettes, ... On top, we do support sending instruction per cassette to Embedding (orientation, decalcification required,...). Dictation / grossing should be the main drivers (instead of only text description).

On behalf of Mario Villace : SW Architect - Roche Diagnostics :

From interoperability point of view, structured gross descriptions & section codes discussion will be helpful as you mentioned but quite complex. IMHO, we can discuss and assess it by defining its scope (as a first step): a quick list (as example) of information we need to code, review the variability of that info and review all available codes systems (SNOMED CT or others) that can be applied on it. Then, we can leverage some of the elements described by HL7, as Laurent propose.

Mario Villace (talk) 11:01, 22 May 2018 (CDT)

Discussion: Use Case #5: Incorporation of Legacy Digital Images for Use in APW

This section seems concerned with migration/parsing of older images (format, etc.), but we may also want to visit the concept of the analogous use case from the order filler (APLIS, etc.) end: that you want to also be able to handle image processing for legacy UID/barcode structures for slides. Would we want to call that incorporation of legacy physical asset preparation data? (Or something to that effect?) (Practical example: at MGH, we use SQ Copath, but Dr. McClintock and our APLIS team exported structured information from our prior LIS, PowerPath, into converted case structures in SQ CoPath. Thus our APLIS had structured data, tied to a PowerPath UID and a SQ UID in the system. We were able to create a rule in our LIS-IMS interface to have our imaging orders send the PowerPath UID to the IMS, so that the scanners reading the old barcodes could correctly identify and associate that slide with its converted case in CoPath. This is incredibly useful for customers that ever changed APLISs or ever will, as prior cases may have requests to be scanned to for use with future cases, i.e. to evaluate for tumor recurrence.)

Discussion: Use Case #7: Quality Control / Quality Assurance and Error Correction Workflows to Support Digital Pathology

NCJ Note: I'm not sure we if we want to consider this its own use-case explicitly; these are workflows inherent to all scanning processes (details will vary by use case the QC/QA process is covering). But these are part of workflow and should be modeled. The other option is to consider this section as modeling for scanning processes in general...

NCJ Note: Quality control and quality assurance are somewhat polysemous terms. See my ppt from shared dropbox area for some details. For clarity here, I will define 3 terms for use within the document. We can debate these if desired.

Definitions: Quality Evaluation (QE): An assessment from a device, software algorithm, or person about the quality of a target physical or digital asset.

NCJ Note: My definition here, just to make the distinction between the common vernacular of QC - as in "he QC'd the image" versus the formal definition of quality control. I'm open to using a different phrase if desired. But an important distinction here is that the scanners and scanning software have internal QE tools, which we would want to discriminate from technician QE, pathologist QE, and potential external algorithmic analytic QEs. Note that the scanner/software/tech QEs have been part of both FDA clinical validations and technical validations. (See FDA technical guidance. Quality Control (QC): A system for verifying and maintaining a desired level of quality in an individual test or process. (From traditional CAP definition. My note: usually implies prospective processes, and to generate data.)

Quality Assurance (QA): Systemic monitoring of quality control results and quality practice parameters to assure that all systems are functioning in a manner appropriate to excellence in health care delivery. (From traditional CAP definition.)

Specimen (Definition from DICOM Supplement 122) A physical object (or a collection of objects) is a specimen when the laboratory considers it a single discrete, uniquely identified unit that is the subject of one or more steps in the laboratory (diagnostic) workflow. Can have parent specimens (or the patient as the ancestor/source) and can have child specimens (i.e. a TAH-BSO had the source/parent of a patient, and children specimens of the uterus, two fallopian tubes, two ovaries, all of which can have multiple blocks, with multiple slides, each which can be scanned.) A specimen could even be materials removed from a slide via laser microdissection. The major thing to understand here is the extensibility of the parent to children relationships.

Container(Also see DICOM supplement): A physical object containing a specimen. This could be the jar filled with formalin holding an excised organ upon delivery to surgical pathology laboratory, the cartridge holding a block (consisting of parrafin wax and tissue cut from the organ/bx), or the slide itself encasing the stained tissue. A container usually only carries specimens from one source, but in some cases could hold specimens of multiple sources (such as a TMA).

-Nicholas C. Jones (talk) 17:53, 13 March 2018 (CDT)

NOTE from NCJ: Because this is so involved, I moved most of the text from the WP area to here and left a summary on the main page.

Notes on identification and QE ontologies: With the exception of in vivo microscopy (beyond the scope of this IHE White Paper, and in this regard, closer to Radiology's paradigm), we should consider the scene or target of an imaging process as a (potential combination of) specimen(s), container(s), and other components of the container(s).

• A bag(container) with a sticker with patient's information (component of bag container) is received at the surgical pathology laboratory. It holds two jars(containers) and in an outer pocket a folded paper requisition which also has a sticker with the patient's information. The requisition is considered a separate object, though it correlates to the specimens in the container.
  • Between the requisition and the jars, the case is accessioned as case SYY-X. The requisition is labeled with the pathology case number SYY-X. If the requisition gets scanned, it should be associated at the case level (for the APLIS), and if put into DICOM format, it would fall under the secondary capture IOD.
  • One jar(container) holds formalin and biopsied tissue (specimen). The jar's sticker has the patient information and "LEFT BREAST 6:00" written on it.
    • Once the case is accessioned, the first jar becomes part A of the new case. The core biopsy is embedded in a block (new specimen, parent of the core bx 6:00-specimen A) labeled as A1.
      • Four slides(containers of new subspecimens) are made from block A1: A1-1,2,3, and 4. Their parent is block A1.
        • Each of these slides is later scanned. Slide A1-3 had a tissue fold which contributes to the the first of two tissue sections on the first scan to be out of focus, so the technician rescans it. The second scan has the has the first tissue section of slide A1-3 in focus, but then the second tissue section of the slide out of focus. In the interest of time, the technician makes annotations on the slides for the pathologist to reference the first scan of A1-3 for one part and the second scan of slide A1-3 for the second. (Note the importance: you may want to keep two scans of the slide. Slides:scans is a 1:n relationship.)
  • The other jar holds a core biopsy specimen and is labeled "RIGHT BREAST 3:00."
    • The second jar becomes part B in the case. The right breast core biopsy is embedded in block B1.
      • Four slides are made from block B1: B1-1,2,3, and 4. Their parent is block A1.
        • All four slides are scanned successfully.

For ease of understanding: quality evaluations could occur for any of these objects at any step in the diagnostic process as part of the greater system of quality control.

• Accessioner/preprocessing QE could note a problem at the receipt part prior to case accession. (Missing or misprinted label, for instance, or an order/delivery problem: perhaps it was a fine needle aspiration biopsy, the bag needs to be delivered to the cytopathology laboratory instead.) Since the white paper's topic is the digital aspects of this, we will skip over most normal processes here. The important point is that we keep the model of the evaluator making a quality evaluation of the target (specimen, container, requisition, etc.) at various points in the process, and each problem could become resolved, generate a warning/advisory, or be unresolvable (i.e. receiving an empty specimen container, which might not generate a surgical pathology case number, but certainly should generate a safety report or other QA trigger).
• So it is important to understand that images could be taken of various targets here:
  • An image of the bag with containing the jars and requisition could be taken to document quality processes (i.e. a half-printed barcode on the label) by a basic camera modality. In this instance, you had an accessioner's QE of the bag trigger a warning (only 1.5 matching labels instead of 2), so the image is taken to document that issue.
    • A specimen could be imaged during grossing and sectioning, resulting in a gross image.
      • The block itself could be imaged, perhaps after microtomy, but prior to being sampled for a molecular diagnostics test. (The block itself could also be imaged after a subsection was removed to document the location of the sampling of the molecular test.)
        • A slide could be imaged in numerous ways:
          • photographed macroscopically by a scanning technician to document that the slide has a large chip/piece missing from it, and that it cannot be scanned in the whole slide scanner.
          • The scanner takes a macroscopic image of the slide to separate the slide label area, and to analyze the coverslipped area for contrast and thus which areas of the slide to scan.
          • The slide is scanned by the scanner, which stitches together micrographs into a WSI, saving them along with metadata and the macro image. Note that the slide could have multiple scans from the same scanner, with the same or different scanning settings, or from different scanners, or pre-destaining and post-destaining. Furthermore, slides can be cut and left unstained for later staining; processes between APLIS and digital pathology systems should include for "update" messages such as a slide being stained, unstained, or restained, or additional slides being cut from the block.

It also must be noted that slides relationships vary:

• Slides with formalin fixed, paraffin-embedded tissue sections generally have the relationship of Patient->(Case/Container)-> Part-> Block-> Slide.
  • Section thicknesses can vary (i.e. 5u vs. 3u) and may affect scanning procedures or success rates.
• A liquid based pap smear would have a different relationship Patient->(Case/Container)->Vial (i.e. Surepath or Thinprep vial)->(Tube, which may be implicit)->Slide.
• A direct smear of a specimen could be Patient->Excised tissue (pre-container)->direct application to slide.
• Whole mount or otherwise larger slides should be modeled in the system. (Some scanners can accept "non-standard" slide sizes, and others cannot.)

Optimal databases and information processes will correctly model different types of slides.

7b. Quality Evaluations for WSI

• Pre-processing QEs
  • Scanning Technician(ST) Orders QE (scan order vs. slide type vs. request/reason type vs. priority vs. location vs. presence of existing scans)
  • ST Slide QE: physical problems with slide? Was the slide broken and repaired (Resolvable or not? Change scanning process or not?) Issues with tissue? (i.e. note presence of air bubble, tissue folds, possible necrosis warranting extended focus, etc.) Fingerprints, dust, extra mounting media on slide? (Can it be cleaned off or not?)
  • ST Identification QE: Identification issues? Identification exceptions warranted? Or ID based rejection? Processes must account for this type of issue by allowing ST manual overrides or alternate processes for slides that require special identification handling.
    • Clinical example 1: scanning a slide from an outside hospital to document a consult case - you do not want your system to automatically read the OSH hospital barcode and make associations based off that, as the OSH barcode/UID # could create a mismatch to another asset for your site.
• Scanning QEs: initialization and during scanning process
  • Scanner QE for robotics/physical issues- sensors check for robotics issues, check for correct placement of slide on stage
  • Scanner QEs for macro image capture or equivalent step (including label/barcode capture)
  • Scanner QEs for tissue focusing and micrograph captures
  • Scanner QEs for stitching, post-processing, saving image
• ST Image QE: is the image adequate? Did the process work correctly?
  • Identification confirmation (data in image/system matches label identifiers and order)
  • Tissue capture confirmation - was all of the tissue captured in the image? (Comparison with macro image of slide, occasionally by comparison to the physical slide, rarely by viewing the slide under the microscope.)
  • Focus/sharpness QE: is the image coarsely out of focus? Do certain areas of the slide have coarse or fine focus problems? This may include the ST evaluating the entire WSI at low power and some areas at high power.
  • Miscellaneous issues: are there problems with stitching, imaging artifacts, issues with color or white balance? Does the appearance of inflammatory processes merit a scan at higher magnification?
  • Networking and image distribution issues: Can the ST get the image to the intended destination? Was upload or transfer successful?
• Pathologist QE (implicit or explicit during MD review) - the pathologist may also check for similar issues, but is more likely to assess quality in the context of the question "is the image adequate for diagnosis?" rather than "did the imaging process occur as intended?" Note there can be multiple pathologist QEs, especially in the case of an academic medical center (resident or fellow reviews case, then attending) or in the case of second opinions (internally or external consultation).
  • Workflows and systems should support documentation of their findings communication from pathologist to the imaging and or slide production areas. (i.e. Please rescan at 40x, please rescan to ensure annotated ROI is in focus, this area needs extended focus/z-stack, please rescan with other scanner, please recut slide without tissue fold and scan that, etc.)
• Administrative or other lab personnel QE: some lab workflows such as for image analysis for receptor studies may warrant QEs of images for those specific purposes. Systems and workflows should also allow for documentation and communication of such findings and for potential orders of rescans or other troubleshooting steps.
• Computer/algorithmic image analysis QE: some systems may have tools for post-scanning analysis of images to determine adequacy (i.e. Hamamatsu Nanozoomer S360 has sharpness/focus evaluator), or a pathology department may have tools to evaluate WSIs in their archive.

Discussion: Use Case #8: Digital Pathology in Support of Clinical Conferences

NCJ Question 1: How do we want to define clinical conferences? I would like to avoid the ambiguity of definitions like this. It may be easier to define through sub-types and examples, which is the approach I'll tentatively take here. But I would definitely like to discuss the tentative definition I'm suggesting here

Tentative definition of clinical conferences(for discussion): meetings of two or more clinicians and/or other clinical personnel, either in person, through tele-presence, or a combination of physical and tele-presence, to discuss and review clinical details of one or more patient's cases for prospective quality control purposes or retrospective quality assurance purposes, within the domain of clinical care for the patient. This does not include academic case studies in settings such as a professional association meeting. Clinical conferences are generally scheduled, as opposed to ad hoc processes, which would more commonly be considered consultations.

Categories include:

• Consensus conferences: common term used for routine conferences in which pathologists review one or more challenging or rare cases with colleagues prior to sign-out. Such conferences may or may not be noted in the final diagnosis of the report. Consensus conferences could occur at a multi-headed microscope, through tele-presence using static, dynamic, or whole-slide images, or any combination of imaging techniques.
  • In a multi-site/enterprise setting, consensus conference through digital pathology may be desirable as conferencing pathologists could be distributed geographically, and digital pathology supporting such conferences can allow for easy, efficient review of pathology images for group review.
  • In some circumstances, we could expect the desired combination of multi-headed microscope use along with digital pathology, such as in the scenario of prior consultation cases which were digitally archived needing to be reviewed along with glass slides at the multi-head. Alternatively, in a primary diagnosis setting, we may expect current cases would be reviewed through digital pathology systems being coupled with glass slides of prior cases (pulled prior to conference, but not scanned) being reviewed at a multi-head.
• Internal quality assurance conferences: Within a pathology department, certain cases may be retrospectively reviewed on an ad hoc and/or systematic basis. For instance, a cytopathology/histopathology QA conference might review cases in which the cytology and histology diagnoses disagreed to find root causes. (Such as issues of interpretation versus issues of sampling variation in cases involving fine needle aspiration biopsies and core biopsies.)
• Tumor boards or multidisciplinary conferences: In these settings, clinicians of multiple specialties review cases together. (Note we may make the distinction between tumor boards and multidisciplinary conferences as in some cases the patient may not have a tumor, yet the case can still warrant a multidisciplinary conference review.) In many instances, these conferences may occur outside the pathology department, so pathologists may traditionally show static images (or commonly a powerpoint with multiple static images), projections of a slide from a microscope, or whole slide images. Note that it is common for radiologists to use thin client viewers to present radiology images, so toggling to thin clients to present whole slide images is often considered highly desirable for such conferences. As the complexity of physical organization of clinicians and interconnected work grows, flexibility in presentation of such conferences is highly valuable to provide for clear, efficient presentation of case materials to ensure high quality conferences that minimize time-related switching costs in such conferences.

Technical notes:

• It is commonplace for slides to be imaged for the purposes of such conferences. Workflows may vary in a primary diagnosis scenario.
• Although such conferences may use "thick clients" for WSI viewers, it may be considered more commonplace to use thin clients for such scenarios. As such, in a thick-client primary diagnosis setting, the determination of a set of WSIs previously scanned may warrant upload of scans to a thin client hosting server, or transmission from a file store or from one thick client to another. (This latter scenario could occur if a hospital used a thin client system for internal client cases, and a separate thin client system for telepathology cases received outside the hospital network.)
• To provide inter-operable vendor support for such conferences, it may be desirable to support modeling of sets of requests for multiple patients to pathology for the purposes of such conferences. Common current practice may involve one or more parties communicating to pathology the request to review cases at the next conference by e-mail, but it may be preferable to allow for systematic requests (i.e. through the EHR) from parties like oncologists to pass from the EHR through interfaces to other systems (APLIS, PACS, and/or digital pathology systems) to assist in administration of such conferences. (Note from NCJ: Do we want to discuss what these orders might look like as HL7 messages? Does anyone know of examples of this?)
• Many digital pathology thin client systems allow for the organization of multiple cases, even for disparate patients, into sets or be indexed together in other forms, which can help assist in the process of organizing rapid, efficient, accurate switching between cases for multiple patients in these settings.
• While conferences are not generally tied to billing, from the perspective of cost accounting (saving multiple physicians time) they are extremely valuable. From the perspective of prospective clinical accuracy and providing constant feedback loops to and between clinicians, they are invaluable.

Discussion: Use Case #10: Image Registration Functions

Regarding 10.c: NOTE FROM NCJ: Does anyone know of any groups using image registration from WSIs/blocks to gross images in a clinical environment? If so, we should separate that out from the "future use" section.) -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

Image registration involves the creation of a cross-image coordinate system of multiple images for the same object(s) or "scene."

• Example for explanation: since many liken WSI to GoogleMaps, let's use GoogleMaps (used here as GoogleMaps + Google Earth functionality) as the example for analogy. Both WSIs and GoogleMaps involve the creation of numerous individual images through an optical and camera system. WSIs involve capturing numerous micographs (each a mosaic of pixels) in a mosaic pattern of micrographs, stitched together, while GoogleMaps took numerous satellite images of the Earth and stitched them together. But GoogleMaps also includes complex image registration algorithms, where images from space were correlated to images of the earth (various types of maps) to create a more complex but more accurate model of the Earth. Together, they allow for easier use of more complex path creation, but also to toggle in a location between a "street map view" and the satellite view of the same location. Image registration functions are used in other areas of medical imaging to correlate multiple modalities of imaging for the same organ(s).

• 10.a. Image registration for swapping to correlated position on different slide from a single block. This feature allows for the user to swap to another slide from the block (i.e. going from A1-1 H&E to A1-2 CK8) to the analogous location on the new slide without the need to visually search for it. Used in a larger series, it allows for oscillating between multiple slides in the same location (ie. A1-1 H&E, A1-2 CK8, A1-3 CK 14, A1-4 ER, A1-5 PR, A1-6 her2... etc.)
• 10.b. Image registration for correlated multi-slide view from a single block. This allows for simultaneous presentation of multiple slides at once off the same block by allowing the user to control the location of one slide and having the system move the view of the other slides to the corresponding locations. (Note: "manual" control/locking of multi-slide views is basically similar here but is not using an automated image registration system to create the alignment of views.)

10.c. Image registration beyond just a series of serial sections of a block have been researched, and although these are (to our knowledge) not currently in clinical use, further possibilities have been documented in research environments. These include creating 3D virtualizations of blocks by registering large series of WSIs, or registration of multiple blocks with gross images and through those to other images such as those from radiology. Vendors, academics, and standards may want to consider these more complex image registration as future possibilities and thus design ontologies and systems that are extensible enough to warrant these use cases in the future.

Note that in the case of doing image registration in multiple slides, this may be considered a loose definition of image registration, as technically the different slides could be considered different "scenes" as a different object is being imaged. But since the slides are different serial sections cut off an FFPE block, it is ideally very close to the same scene (with ~5 um or even less between serial sections). Still, that difference between the slides makes these image registration processes more challenging, as variations between the levels off the block will show small variation in shape, size, and features from other slides.

• It is important for the success of such algorithms for systems to pass identifying metadata not just on unique slide identifiers, but also slide section thickness (such as 5 um), block identifiers, and tissue cut order (i.e. A slide called "A1-7 H&E" on the label may mean the 7th slide off the block "A1," but its unique identifier may not itself indicate that this slide is the 7th off the block, especially if the APLIS unique identifiers are created automatically in the database by order of their creation as a database asset rather than physical cut order.)
• Furthermore, tools for manual intervention to change orientation of tissue may be required to aid these algorithms. For instance, original H&Es may have been cut with epidermis facing in one direction, while the subsequent cuts for IHC may have a different orientation. Tools to permanently rotate images in multiples of 90 degrees, or temporarily rotate images to aid in image distribution may assist in these processes and be part of active troubleshooting, as image registration may be done on-demand by technicians prior to passing WSIs onto pathologists.

Discussion: Use Case #11: Digital Pathology in Support of Intraoperative Procedures

I think we could batch frozen section interpretations and rapid FNA adequacy assessments here together, but it anyone wants to split them into different use cases, that would be fine as well. -Nicholas C. Jones (talk) 15:24, 13 March 2018 (CDT)

I also think we should note that frozen section and rapid FNA slides often require additional steps for identification. Some sites may only manually write on the labels here, or may later print labels to affix to these labels. At the time of the intraoperative interpretation of the images, such slidse may not have optimal, formal, automated identification set up, so systems should allow for identifcation exception handling here and allow for reconciliation later in the process (i.e. after permanents come out). Lack of formal workflow or system design here can create opportunities for error, and good process design will allow for quality metrics that can be reviewed as part of QC/QA processes.

Discussion: 3.3 Specimen Processing in Anatomic Pathology Workflow

The diagram in section 3.3 of the most recent draft of the white paper (outline draft 0.5, linked on my dropbox shared file also available on the main page) was in my opinion a good start. But I think we need to formally break that down more if we want to be able to abstract workflow steps and thus actors/transactions. Furthermore, the diagram only describes basic up front surgical FFPE slides, so it's missing intraoperative slides (frozens and smears created during fx processes, rapid FNA slides), later requests to stain previously cut but unstained slides, later requests to destain and restain a slide, cytology slides, hematopathology bone marrow aspirate smears, and so forth. These processes may also warrant discussion with the DICOM WG 26. -Nicholas C. Jones (talk) 08:28, 19 May 2018 (CDT)

Discussion: Actors

I started here with the "IHE APW REDESIGN Day 2 v2. pptx" file (shared in my dropbox folder). I may be missing some of the context here since I joined after that meeting (Nov 2017)- if so, I apologize.

Referenced in that ppt, along with formal definitions from IHE glossary:

• Order Placer - Actor that receives and processes (fills) orders. It also receives order cancellations.
• Order Filler – Generates orders for various departments and distributes them. (APLIS.)
• Automation Manager –
  • Definition 1: Schedules and manages operations on biological specimens on a set of robotic devices in a clinical laboratory.
  • Definition 2: A system or component that manages the automation in the laboratory or a part of it. Automation involves the integration or interfacing of automated or robotic transport systems, analytical instruments, and pre- or post-analytical process equipment such as automated centrifuges and aliquoters, decappers, recappers, sorters, and specimen storage and retrieval systems. This actor receives work orders from the Order Filler. It manages the processing of the ordered tests on the appropriate devices and sends technically validated results back to the Order Filler. This actor must be considered even if it manages a small part of the analytical process; e.g. if it manages one single analytical instrument. Multiple Automation Managers can be related to one Order Filler. The Automation Manager can match unexpected results produced by an analyzer with the appropriate incoming Work Order or create a new Work Order to fit the unsolicited observations and send them to the OF.
• Performed Procedure Step Manager - A system that re-distributes the Modality Performed Procedure Step (MPPS from DICOM!) information from the Acquisition Modality or Image Creator to the Department System Scheduler/Order Filler and Image Manager.
• Acquisition Modality - Acquires medical images, waveforms or measurements while a patient or specimen is present (e.g., a Computed Tomography scanner, a specimen microscope or a hemodynamic measurement system).
• Evidence Creator –
  • Definition 1 - Creates evidence objects such as derived images, presentation states, Key Image Notes, and/or measurements (Evidence Documents), and transmits them to an Image Archive.
  • Definition 2 - A system that creates additional evidence objects such as images, presentation states, Key Image Notes, and/or Evidence Documents and transmits them to an Image Archive. It also makes requests for storage commitment to the Image Manager for the data previously transmitted. It may also retrieve worklist entries for post-processing steps from the Post-Processing Manager and provide notification of completion of the step, allowing the enterprise to track the status of post-processing work.
• Image Manager
  • Definition 1: Manages and provides access to stored imaging objects.
  • Definition 2: Stores DICOM objects without guarantee of long-term storage.
  • Definition 3 (For Image Manager/Archive): A system that provides functions related to safe data storage and image data handling. It supplies image availability information to the Department System Scheduler. It is always grouped with an Image Archive to provide long term storage of images, presentation states, Key Image Notes, and Evidence Documents.
• Image Archive - Provides long term storage of imaging data such as images, measurements, presentation states, and manifests (e.g., a PACS).
• Image Display
  • Definition 1 - Queries for, retrieves and displays imaging data.
  • Definition 2 - A part of a system that can access imaging evidence objects (images, Presentation States, Key Image Notes, Evidence Documents) through network query/retrieve or reading interchange media and allow the user to view these objects.

There were some actors described there that I could not find the definition for:

• Acquisition Manager
• Preparation Manager
• Image Analyzer

Looking through the Radiology IHE documents, I thought the following actors there might be relevant to our purposes here:

• Change Requester – A system that communicates changes to an Image Manager / Archive, indicating that certain imaging instances should be deleted. In addition, it may also send new versions of these imaging instances containing corrected information.
• Document Consumer – The Document Consumer Actor queries a Document Registry Actor for documents meeting certain criteria and retrieves selected documents from one or more Document Repository Actors.
• Document Registry – The Document Registry Actor maintains meta-data about each registered document in a document entry. This includes a link to the Document Repository where the actual document is stored. The Document Registry responds to queries from Document Consumer Actors about documents meeting specific criteria. It also enforces some healthcare specific technical policies at the time of document registration.
• Document Repository – The Document Repository Actor persistently stores documents. It assigns and maintains a unique identifier for each document, to allow Document Consumers to retrieve them.
• Export Manager – A system that can de-identify and pseudonymize the attributes, and optionally the pixel data, of a selected list of instances, before exporting them.
• Export Selector – A system that allows a user to select one or more instances, series or studies for export, for a specific purpose, with a specific disposition, optionally with the inclusion of additional information.
• Imaging Document Consumer – The Imaging Document Consumer Actor parses an imaging manifest document that is retrieved by the Document Consumer Actor from the Document Repository Actor, and retrieves DICOM SOP Instances referenced within that manifest from the Imaging Document Source Actor.
• Imaging Document Source – The Imaging Document Source Actor is the producer and publisher of imaging documents. It is responsible for providing imaging documents and meta- data to the Document Repository Actor, which subsequently registers the imaging documents with the Document Registry Actor. It also supports the retrieval services for DICOM SOP Instances referenced in a published imaging manifest document.
• Importer – A system that imports evidence objects such as images, presentation states, Key Image Notes or Evidence Documents from hardcopy or digital media.
• Portable Media Creator – This actor assembles the content of the media and writes it to the physical medium.
• Portable Media Importer – This actor reads the DICOM information contained on the media, and allows the user to select DICOM instances, reconcile key patient and study attributes, and store these instances. The actor grouped with the Media Importer can then process the instances.
• Post-Processing Manager – A system that provides functions related to post-processing worklist management. This involves the ability to schedule post-processing worklist items (scheduled procedure steps), provide worklist items to post-processing worklist clients, and update the status of scheduled and performed procedure steps as received from post-processing worklist clients.
• Receiver – A system that can receive exported instances over the network, whose behavior is otherwise unspecified unless grouped with other actors.
• Initiating Imaging Gateway – The Initiating Imaging Gateway Actor proxies Imaging Document Set Retrieve requests from an Image Document Consumer to a Responding Imaging Gateway with a Cross Gateway Retrieve Imaging Document Set transaction.
• Responding Imaging Gateway – The responding Imaging Gateway proxies Cross Gateway Retrieve Imaging Document Set requests from an Initiating Imaging Gateway to an Imaging Document Source with an Image Document Set Retrieve request.

Discussion: Transactions

Again, starting from the ppt from the Sardinia meeting. I am going on the assumption here that "Acquisition Manager" meant "Automation Manager" for imaging processes; if this is not correct we need to discuss further. Furthermore, as best as I can understand it, we should assume the "Automation Manager" includes functions both of automated decision making and human decision making. The overall role of that actor seems to be analogous to 2 major functions in radiology: first, the scheduling management of imaging modalities (imaging devices) for procedures - thus the decision making of translating an imaging order to an imaging process order with a specific device destination in mind, and communicating ordering information to that device.

That latter piece may have been described in the Sardinia documentation as the "Preparation manager" - but that role is not, to my knowledge, defined either, so I wrapped that into "automation manager" as well. I apologize if I'm missing something previously resolved; if this is the case, please correct me.

For all references to specific lab transactions, I am referencing the Sardinia document, but I believe we should revisit these to make sure we're all on the same page.-Nicholas C. Jones (talk) 09:04, 19 May 2018 (CDT)

Order Filler - Automation Manager Transactions

• (Imaging Request) Order filler issues an acquisition request to digitize glass slides or macroscopic specimen.
  • Draft: LAB-21 WOS broadcast
  • NCJ:
• Automation Manager responds to order filler with a status code that indicates digital image has been acquired
  • Draft: LAB-23
• Automation manager requests status of a Work Order Status (WOS) (successful completion, normal operation, in error status, location etc.) of digital image creation corresponding to imaging request
  • Draft: Maybe adapt from LAB-26
  • Note from NCJ: should this be a pull or a push? Wouldn't we want the modality set up to be pushing status updates to the automation manager?
• Automation manager queries order filler for acquisition request corresponding to unannounced asset encounter in acquisition device (LAB-22)
  • NCJ: This is a really good point, and what I mean about unscheduled workflow (as opposed to schedule workflow, or SFW, as described in radiology profiles). This brings up interesting problems of design, because if you have scanners just push to the system in an automated manner, bad inputs (i.e. a consult slide with OSH identifiers) could propagate to the wrong patient. In my opinion, any "push" or "implicit order" scenario either needs some additional safeguards for identification exception handling. (Perhaps have all things wait for release or
• Assumption: there exists local slide specimen, container identifiers (associated with a case accession number)
  • NCJ: we want to have contingency plans for other scenarios, and for when people make mistakes. (Discussion of ID exception handling and "virtual labels" multi-identification warranted here.)
• To do: include use cases that need these transactions