https://docs.pathomation.com/pma.core/3.0.2/ 2026-04-17T17:49:29+0300 https://docs.pathomation.com/pma.core/3.0.2/ https://docs.pathomation.com/pma.core/3.0.2/lib/tpl/dokuwiki/images/favicon.ico text/html 2022-03-29T16:03:12+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=21_cfr_part_11&rev=1648558992&do=diff 21 CFR part 11 compliance PMA.core was developed with the FDA 21 CFR part 11 guidelines in mind. Our software adheres to the following principles: * Data will be formatted to allow transfer to another system for long-term storage in a common portable format either during the life of the system or after the system is retired text/html 2022-09-13T12:12:52+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=21cfr11&rev=1663060372&do=diff See 21 CFR part 11 compliance. text/html 2023-11-21T17:50:43+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=access_control&rev=1700578243&do=diff Access control Forms can be specified to apply to only specific root-directories. Click on the “Form accessibility” button in the forms metadata view: You can now see a roster containing all available root-directories along the X-axis, along with all available forms on the Y-axis. text/html 2022-02-11T19:01:56+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=accessing_data_on_a_network&rev=1644595316&do=diff Root directories, mounting points, and network data It is common that WSI data is not stored on the local drive, but on a shared (high-capacity) storage device. There are several reasons why this may be the case: * This machine may collect files from different locations and/or scanners. text/html 2022-09-15T19:55:53+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=acl&rev=1663260953&do=diff See Root directory security text/html 2023-11-27T13:51:44+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=active_sessions&rev=1701082304&do=diff Active sessions The currently active users are displayed in 'session management'. The system allows admins to terminate a user's session. The lifespan of a session is governed by the ASP.Net session timeout value. This value is displayed in the installation check page. When a session is idle for longer than the session time out value, it is automatically ended and the corresponding user will need to log in again. text/html 2023-11-21T17:13:55+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=adding_a_copyright_to_snapshots&rev=1700576035&do=diff Adding a copyright notice to snapshots The following operations should only be performed by experienced users. If you don't know where or how to find a file called “App_Data\Data\PMACore.config”, you should stop reading and contact somebody more knowledgeable in this area. text/html 2022-10-07T10:19:44+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=anonymization&rev=1665127184&do=diff Anonymization and pseudonymization PMA.core is the guardian of sensitive information. The following features are present to manage data anonymization: Viewport configuration (PMA.UI) When presenting a viewport to serve slide content, one can opt to hide the necessary visualization elements in the viewport that could lead to inadvertently revealing sensitive information: both the label (barcode) and filename widgets can easily be hidden with a single line of JavaScript code. Check our text/html 2022-11-29T14:45:13+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=audit_trailing&rev=1669722313&do=diff Audit trailing An audit trail (also called audit log) is a security-relevant chronological set of records that provide documentary evidence of the sequence of activities that have affected at any time a specific operation, procedure or event. In PMA.core audit trailing is implemented as part of text/html 2023-01-13T13:01:59+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=barcode&rev=1673604119&do=diff Barcodes Microscope slides have labels. In many instances, these slides have barcodes printed on them. In complex scenarios, a single label can even have multiple barcodes. These barcodes are available in several different industry-standard formats. Through the technique of Optical Character Recognition ( text/html 2023-11-27T18:27:02+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=caching&rev=1701098822&do=diff Caching For optimal performance, PMA.core supports both tile cache and cloud cache. Our policy is that caches are deleted automatically after a retention period and no new cache is created if there is not enough disk space. There's a separate configuration page for cache settings Tile caching text/html 2022-08-22T13:53:21+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=compression_type&rev=1661165601&do=diff Compression types PMA.core supports the following CODECs: * Blosc * BMP * Deflate * iSyntax * JPEG * JPEG2000 * JPEGXR * lossless * LZW * PNG * RLE In addition, for select file formats we also indicate the level of compression used, which is particularly useful when using lossless compression. text/html 2022-01-17T14:09:51+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=crud&rev=1642417791&do=diff CRUD (Create Read Update Delete) principles PMA.core extends the CRUD acronym to become: CRUUDD. This means: * Create * Read * Update * Upload * Download * Delete CRUD principles will be introduced in PMA.core 3. Stay tuned for more information text/html 2022-01-17T14:10:13+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=cruudd&rev=1642417813&do=diff See crud text/html 2022-09-27T16:34:57+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=diag_elmah&rev=1664285697&do=diff Elmah ELMAH (Error Logging Modules and Handlers) is an application-wide error logging facility that is completely pluggable. This offers a standard way of capturing runtime errors in software, and they can help troubleshoot intermittent problems. Examples include: * connection information is (temporarily) no longer correct text/html 2022-04-01T13:03:57+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=diag_performance&rev=1648807437&do=diff Performance In the Diagnostics -> Performance page you can inspect a statistical measure of the performance of PMA.core. The page displays the average time it takes for PMA.core to serve a request. The page is split in two parts one for hourly averages text/html 2023-11-21T18:12:39+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=external_api_data&rev=1700579559&do=diff External API meta-data Oftentimes you have external data coming from a REST HTTP API and want access to it through the Pathomation software platform for digital pathology and virtual microscopy. Importing the data as Pathomation form data may not always make sense for a variety of reasons. text/html 2023-11-21T18:00:53+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=external_data&rev=1700578853&do=diff External meta-data Oftentimes you have external data in a separate repository and want access to it through the Pathomation software platform for digital pathology and virtual microscopy. Importing the data as Pathomation form data may not always make sense for a variety of reasons. text/html 2023-01-17T17:02:41+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=fluo&rev=1673964161&do=diff Fluorescent data PMA.core supports various fluorescent file formats. To get a list of most recent supported formats, have a look at <https://www.pathomation.com/formats>. Histogram clipping The software offers the option to clip a fluorescent channel within a range of intensity values (min/max). In other software, this range is typically set to the pixel depth of the image (8, 16 bits etc.). Other times it is set to the actual min & max values within the pixel data of the image. Our approac… text/html 2023-11-21T17:23:48+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=form_management&rev=1700576628&do=diff Forms In the forms tab, the list of available forms is displayed. It is possible to create new forms or edit the existing ones. Next to each existing form, several options are available: * Delete: Deletes the form. This option is disabled if user data has already been submitted for this form. text/html 2022-11-22T12:47:27+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=format_omnyx&rev=1669110447&do=diff Handling legacy Omnyx JPEG 2000 exports General Electric's Omnyx scanner vendor company supported two file formats: a native format with RTS extension, and an exported JPEG 2000 format. We found out by working with several of our customers that the JPEG 2000 exports are not always reliable. In a couple of instances, the used encoding causes memory problems. We attribute this to a faulty use of the encoder originally used by the vendor. text/html 2022-11-22T13:10:53+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=format_tiff_jpeg&rev=1669111853&do=diff Working with flat TIFF or JPEG files Our software can read flat TIFF and JPEG files. If you're using these file formats to work with gross (macroscopic) imaging data, you should be just fine. However, for the sake of backward compatibility with standard image editing software (anything ranging from MS Paint to Adobe Photoshop), some vendors allow export to text/html 2022-11-22T12:16:38+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=format_troubleshoot&rev=1669108598&do=diff File format troubleshooting There are any number of ways that information can be encoded. While we strive to support as many file formats as possible, we can't promise you that we support everything. Occasionally, you'll encounter data that you think should work, but for whatever reason, text/html 2022-11-22T12:47:07+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=format_ventana_bif&rev=1669110427&do=diff Ventana BIF slides Two variants exist of the Ventana BIF file format: * One variant that was produced by scanners manufactured before 2015, and that required both a TIFP and a BIF file file to be rendered correctly * A single file BIF variant used by the new scanners manufactured after 2015 text/html 2023-03-20T15:28:55+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=forms&rev=1679315335&do=diff Forms See Form management. text/html 2022-02-04T21:14:23+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=geo-replication&rev=1643998463&do=diff Geo-replication text/html 2021-07-20T16:19:59+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=honest_broker&rev=1626787199&do=diff Honest broker concept PMA.core software acts as an honest broker between the various vendor-dependent file formats on one end, and a variety of different end-user applications on the other: The end-user applications are typically referred to as “downstream” applications in this manual. They can be other member-components of our platform ( text/html 2026-03-10T11:43:50+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=ifu&rev=1773132230&do=diff Instructions For Use (IFU) To view the IFU document which is provided as a PDF, you need a PDF viewer such as Adobe Acrobat Reader. The program can be downloaded free of charge via https://get2.adobe.com/reader. Download the IFU documentation: https://docs.pathomation.com/ifu/pma.core/3.0 text/html 2023-11-21T13:56:20+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=image_management&rev=1700564180&do=diff Image management The image manager is accessible from the “Images” option on the left menu. This section allows the user to browse through the available virtual slides, launch the built in slide viewer, manage cache files, view, move and rename each image. text/html 2023-11-21T16:22:21+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=image_manager&rev=1700572941&do=diff Image management The image manager is accessible from the “Images” option on the left menu. This section allows the user to browse through the available virtual slides, launch the built in slide viewer, manage the cache files, view, move and rename each image. Tree view (left panel) text/html 2022-03-14T19:19:11+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=image_manager_left_menu&rev=1647274751&do=diff Image management - left dropdown menu Using the tree view the user can navigate through the available directories. The dropdown menu in the top left part of the tree view provides convenient access to certain managerial tasks related to the image management view. Root directories text/html 2022-03-14T19:31:47+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=image_manager_mid_menu&rev=1647275507&do=diff Image management - middle dropdown menu In the Image manager, clicking on a directory will display its contents in the middle section. The dropdown menu in the top left part of the slide listview provides convenient access to certain managerial tasks related to the text/html 2022-10-13T10:41:21+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=impact_of_tile_quality_on_data_traffic&rev=1665646881&do=diff Impact of tile quality on data traffic Using Image Settings, one can control the quality of individual tiles. Each tile is a JPEG-image, and the setting controls the compression-rate used to generate these JPEGs. We did a survey of the impact of various quality settings, and came up with the following measurements. As could be predicted, reducing the tile quality significantly reduces the amount of bytes transferred: text/html 2023-11-27T17:30:04+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=installation&rev=1701095404&do=diff Installation Installation typically takes about half a day, but may vary depending on the need to download and install additional prerequisites, as well as internet (wifi) speed provided, and the performance of the hardware setup. The various components are of PMA.core and the terminology used throughout this wiki are outlined in the following schema: text/html 2022-08-06T14:46:15+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=installation_check&rev=1659786375&do=diff Installation check The installation check section performs various tests to ensure the correct installation of the system as well as to verify the presence of all the required libraries. Several of these parameters are only available from PMA.core 1.1 and onwards, including: Operating System, IIS version, Application init time, Allow nested text/html 2022-04-11T12:57:02+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=integrity_report&rev=1649671022&do=diff Integrity report The integrity report section will perform a recursive scan on the selected root directories and report virtual slides that cannot be parsed by the system. To perform an integrity check you simply * select one or more root-directories to be scanned at the time text/html 2023-11-27T17:39:44+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=interfacing_the_server_from_3rd_party_software&rev=1701095984&do=diff Interfacing with PMA.core from 3rd party software PMA.core is a very flexible product & can be interfaced with from a number of other environments. While an exhaustive guide on how to interact with PMA.core from every possible software is outside the scope of this document, we offer a short outline of the various types of interaction here. text/html 2023-11-24T18:56:05+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=license_expiration&rev=1700841365&do=diff License expiration When your license has expired or has become invalid for any other reason, you can still keep using the software. You receive a notification of this after logging in: In addition to this administrative message, the tiles served through the tile server are greyed out. Each tile is also provided with a notification warning, making it obvious and that you should text/html 2023-11-27T17:24:55+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=license_setup&rev=1701095095&do=diff License setup Follow the steps in this part of the wiki when you: * are a first-time user of PMA.core and don't have a license file yet * have an expired license file * move your PMA.core setup to new hardware or virtual machine * upgrade your commercial agreement with Pathomation to facilitate more concurrent users text/html 2022-03-28T16:05:24+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=licensing&rev=1648472724&do=diff License handling This wiki entry is about the technical aspects of licensing in PMA.core. Pathomation's license policy is described on its website. Are you dealing with an expired license? See the procedure on license renewal. Pathomation has a software licensing scheme that involves the exchange of license files. text/html 2022-04-04T12:03:48+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=logs&rev=1649063028&do=diff Logs The log file section provides access to the raw log files produced by the server. This page page always displays log files available in a reverse chronological order so the latest log file is always on top. You can change the number of log files presented using the text/html 2023-11-21T17:42:52+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=look-up_lists&rev=1700577772&do=diff Field types and lookup lists Field type Description Displays a text box that accepts free text entry Displays a text box that accepts an integer value Displays a text box that accepts a decimal value Displays a text box that accepts date & time value text/html 2023-11-21T16:49:43+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=manipulating_slides&rev=1700574583&do=diff Manipulating slides Whole Slide Images comes in a variety of (physical) shapes and sizes. Some file formats (like Zeiss ZVI or Nikon ND2) can represent no more than a (multi-fluorescent channel) snapshot. Other formats can be very complex and consist of multiple files and directories. text/html 2023-11-21T17:18:06+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=meta_data&rev=1700576286&do=diff Meta-data With meta-data, we identify all non-graphical data about a slide. The actual pixels (or viewport representation) of a slide are not meta-data. Annotations can be considered meta-data in the semantic sense, however they're linked to graphical data. Therefore, text/html 2023-11-21T15:35:52+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=minimal_user_management&rev=1700570152&do=diff Getting started PMA.core is a web-based system running on IIS. Therefore, you'll need a web browser and a network connection to use the system. During installation you will have determined the URL through which the application is accessible. Navigation text/html 2022-10-13T10:50:03+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=misc&rev=1665647403&do=diff Miscallenous topics Advanced customization Depending on your license terms and specific installation, you may see more or less additional columns behind the login. E.g., you may have a restrictive version that doesn't allow you the granularity to determine which users may perform annotations and which ones may not. In that case, the column 'Can Annotate' will not be visible for your particular installation. You should text/html 2023-11-21T16:07:56+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=monitoring_system_use&rev=1700572076&do=diff Monitoring system use On the main page, you can see a chart that indicates recent system use. PMA.core provides access to its logging system and presents detailed and precise information and statistics about the server's usage. This is done using PMA.core's internal logging system without using any external analytics library like Google Analytics text/html 2023-11-27T18:35:21+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=nonapi&rev=1701099321&do=diff Image Endpoints The following endpoints are available in PMA.core to view Whole Slide Images and their associated labels, thumbnails and macro images. The following list contains the endpoint URL, a brief description and the available parameters for each one. text/html 2023-01-16T17:22:03+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=pmann&rev=1673878923&do=diff The Pathomation ANNotation interface PMANN is a part of the Pathomation back-end API that makes it easy to handle heterogeneous (external) annotations. PMA.core can leverage the use of PMANN via the External Files interface and the associated API calls. These API calls associate a number of files containing any known 3rd party annotations with a slide. PMA.core supports 3rd party annotations from the following vendors Visiopharm, Indica Labs and Aperio. Each of these formats are supported via… text/html 2023-09-26T18:01:33+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=release_history&rev=1695740493&do=diff Release history Version Revision Released PMA.UI version Documentation PMA.core 3.0.2 (current version) c8db6e48 January 2023 2.26.5 Wiki PMA.core 3.0.1 be720dc8 November 2022 2.21.0 Wiki PMA.core 3.0.0 f47dcd30 May 2022 2.21.0 Wiki PMA.core 2.0.2 2081 March 2022 Wiki PMA.core 2.0.1 2069 February 2022 text/html 2023-11-27T13:59:00+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=report_events&rev=1701082740&do=diff Events PMA.core offers an internal event logging system for actions requested by the server. The logged types of events are : * Image: A user requested a slide information, usually through the ImageInfo API call * Form: A form was created, requested or data was submitted to a form by a user text/html 2023-11-27T13:54:55+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=report_heatmap&rev=1701082495&do=diff Heatmap statistics The heatmap of a slide is a statistic calculated by PMA.core that shows the regions that users view most frequently in a slide. It can be used to find the interesting regions (or at least the regions interesting to your users...) of your hosted slides. This is displayed in a colorful image with more reddish colors indicating highly trafficed regions. At the bottom of the heatmap you can see the color legend which describes what each color indicates in terms of the number of r… text/html 2023-11-27T13:57:50+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=report_monthly&rev=1701082670&do=diff Monthly statistics [ ] On the monthly statistics page you can generate monthly reports for the server's activity over a specified range of time. These reports include: * Number of active users per month * Number of slides viewed per month You can also generate reports by filtering the results by the following criteria: text/html 2023-11-22T17:46:19+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir&rev=1700664379&do=diff Root directories In order for PMA.core to show content, you need to set up root directories. A root directory is a starting location from which your various whole slide images will be hosted. Working with root directories offers several advantages: text/html 2022-09-15T11:33:36+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_azure&rev=1663230816&do=diff Azure storage Azure storage Microsoft Azure has its own protocol, and so we provide a separate mounting point type of it. Let's say that you have an Azure container defined and put some slides in it already: You can convert these credentials in a connectionstring: text/html 2023-11-21T16:08:47+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_config&rev=1700572127&do=diff Root directory configuration Each root directory is given an alias by which it is referred. The alias must be unique, irrespective of its casing. This means that if you have a root directory with an alias “RoOt”, you cannot also have another root directory with a alias text/html 2023-11-21T16:15:44+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_geo_replication&rev=1700572544&do=diff Root directories and geo-replication Cloud providers typically offer different geographical data centers. During setup you can point to any one of these. Then when you want to offer global access to WSI data, you can store the data in multiple zones. text/html 2022-08-06T19:30:29+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_local&rev=1659803429&do=diff Root directories: Local hard disk entry points Configuration If you want to expose a local folder on the server's hard disk as a root directory in PMA.core, you have to give the IIS user account access rights to the folder using the Windows Explorer: text/html 2022-08-06T19:33:33+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_network&rev=1659803613&do=diff Root directories: Network storage Configuration Pathomation runs under a certain application pool. This application pool is associated with a user identify, which may not have access to the network path that you try to access. Giving access for the application pool to access the network resource may be difficult for a variety of reasons. text/html 2022-08-08T17:01:16+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_s3&rev=1659967276&do=diff S3 storage Configuration PMA.core is one of the few vendors that supports cloud storage natively. Let's say that you have an S3 bucket and put slides in it: To protect access, you should create a dedicated entity that can only access that content. You can then create a pair of dedicated access / secret keys for the new entity: text/html 2023-11-21T16:14:39+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=rootdir_security&rev=1700572479&do=diff Security Security is increasingly important. As PMA.core has been deployed in ever-more complex scenarios over the years, its security features have evolved, too. Security pertaining to root-directories is situated at two levels: * Security features that enable root-directories to access content, such as: text/html 2023-11-21T16:02:00+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=security&rev=1700571720&do=diff Security Even more important than file format and storage support, you want to make sure that your data are safe. Many solutions out there require you to take shortcuts around security, or force you to violate your own rules. Pathomation was built with security in mind from the ground up. text/html 2023-11-22T16:44:31+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=settings_image&rev=1700660671&do=diff Image settings In the Image Settings section, image compression and tile related values can be configured. Image settings Field Description Tile size The size of each side of the served tiles in pixels. A value of 400 indicates that the resulting tiles will be 400 x 400 pixels in size text/html 2023-11-22T17:37:54+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=settings_instances&rev=1700663874&do=diff Instances This page shows a list of configured instances of PMA.core. An Instance of PMA.core is an installation of PMA.core that shares the same database as part of a group of Instances. This section is particularly relevant in the context of geo-replication scenarios. Usually each Instance is a replica of PMA.core at a different server and location. You can set an Instance as the current running in this page by clicking on the text/html 2023-11-22T17:58:07+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=settings_scripts&rev=1700665087&do=diff External script External scripts are a method provided by PMA.core to configure and execute command line programs via PMA.core itself. Adding a new script To configure a new script you need to provide the following information describing the application you want to execute and the parameters passed to it text/html 2023-11-22T17:32:47+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=settings_server&rev=1700663567&do=diff Server settings In this section, various aspects of the server behavior can be configured and controlled. Email settings Change settings about the email's sent by PMA.core Setting Description Use Two Factor Authentication Whether to enable two factor authentication for logging in text/html 2023-11-27T17:23:37+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=sidebar&rev=1701095017&do=diff About PMA.core * Who should read this * Storage management * Image management * Release history * Supported file formats Getting started * IFU * Security Monitoring system use Root directories * Configuration * Security (access, ACL) * Geo-replication Image management * Looking at content * Manipulating slides * Transfer (upload/download) * Working with annotations * Adding a copyright to snapshots Meta data * Forms * Field types and look-up lists * … text/html 2024-03-25T16:22:31+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=start&rev=1711372951&do=diff About PMA.core 3.0.2 PMA.core manages your whole slide images. It operates through web protocols and supports a number of file formats, allowing you to manipulate WSI data from different vendors in a standardized manner. This enables efficient management of digital slide images while requiring minimal setup. text/html 2023-11-21T13:50:08+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=storage_management&rev=1700563808&do=diff Storage management Storage is important in digital pathology. Image data can be subject to any of the 3 (or 5) Vs of data science: * Variety - Imaging data in pathology is generated during biopsies (macroscopic observations on the sectioning station), brightfield microscopy (high-resolution), immuno observations (multiple channels), and z-stacking. text/html 2023-11-21T17:48:47+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=submitted_data&rev=1700578127&do=diff Submitted data The data submitted by each user for each form can be obtained in the “Submitted data” tab in the following formats: * * * * (Atribute-Relational file format) HTML Clicking on the “export to HTML” format will take you to an interactive hmtl page displaying all submitted data. Here you can see the data in a tabulated format, with pagination and a search feature. This is very useful for quick inspection and searching for specific data. text/html 2023-11-21T14:09:57+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=supported_file_formats&rev=1700564997&do=diff Whole slide images and virtual slides PMA.core supports a variety of image capturing techniques and modalities. A full list of currently supported formats is available at https://www.pathomation.com/formats. You can read more about our philosophy regarding the support of vendor-specific file formats text/html 2024-02-06T17:38:57+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=system_requirements&rev=1707230337&do=diff System requirements Operating system and software prerequisites In principle any version of Windows + Internet Information Server (IIS) will do. We've got the software to run on IIS Express edition for demonstration purposes. We offer the following formal guidelines: text/html 2022-09-06T10:46:28+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=terminology&rev=1662450388&do=diff Terminology and glossary As with any technology, there are lots of terms we toss around to explain things. Just understanding what each term means can be half the battle. Whether you are entirely new to PMA.core or have been using it for years, there are always new terms to learn. The fact that we use common English words for many capabilities can add an additional layer of confusion. text/html 2023-11-21T17:01:04+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=upload&rev=1700575264&do=diff Transferring slides (upload/download) PMA.core provides built-in upload- and download-capabilities. While not as feature-rich as PMA.transfer; if you quickly want to copy a large volume of slides from one server to another, PMA.core has you covered. One unique feature of slide transfer in PMA.core is that you can use this to copy slides text/html 2023-11-21T18:37:47+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_config&rev=1700581067&do=diff Configure user accounts Add new user accounts To add a user click on the “Add” button on the top right of the table. The following fields can be defined for each user: Field Description First Name The user's first name Last Name The user's last name text/html 2023-03-28T11:50:40+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_cruudd&rev=1679993440&do=diff Permissions PMA.core supports 7 different types of permissions on Root Directories, that can be applied to a user or a group. Those types are: * Create: This grants permissions to create folders, subfolders in a root directory. * Read: This grants permissions to read slides and the contents of all folders in a root directory. Also grants the permissions to read annotations from slides in a root directory. text/html 2023-11-21T18:45:09+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_groups&rev=1700581509&do=diff Groups PMA.core supports user “Groups” which you can find under the User management -> Groups menu. A Group is simply a named list of users in which you can apply permissions. There is a special Group named Everyone which cannot be deleted or edited, which every PMA.core user is always a member of text/html 2023-11-21T18:32:15+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_management&rev=1700580735&do=diff User management PMA.core works with user accounts. Users can be marked as “Administrative”, in which case they can log into PMA.core directly and administer settings for themselves and for others. Users that do not have the “Administrative” text/html 2022-03-25T20:07:53+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_monitoring&rev=1648228073&do=diff User monitoring Overview table * The “Last login” column displays each user's last successful login date. * The “Local” column indicates whether or not a user is managed by PMA.core or LDAP. * The “Administrator” column indicates whether or not a user can access PMA.core. Non administrator users cannot perform system management tasks within PMA.core. text/html 2022-03-07T17:53:02+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_service_accounts&rev=1646664782&do=diff Service accounts Pathomation has a licensing model based on user concurrency. We acknowledge at the same time that there are a number of scenarios where you can have a LOT of concurrent use of the software: * You're hosting a conference or workshop. * You're hosting a webinar with discussions. text/html 2023-11-22T12:23:37+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=user_states&rev=1700645017&do=diff User states A PMA.core user can be in one or more states defined here Administrator The user is an Administrator and has access to the Administrator UI of PMA.core, as well access to all admin API features Suspended The user is suspended from all operations, he cannot login or perform any text/html 2023-11-21T16:45:17+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=viewport&rev=1700574317&do=diff Looking at content (PMA.UI viewport) PMA.core incorporates the PMA.UI framework, which includes a versatile viewport for exploring slides. PMA.UI's viewport is web-based and independent; the front-end runs in the webbrowser of your choice. You can use it to examine brighfield, fluorescent, and z-stacked slide content within the same environment. text/html 2021-06-29T13:39:01+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_1.1.0&rev=1624963141&do=diff What's new in version 1.1? PMA.core 1.1 is revision 784 of the PMA.core codebase. It follows PMA.core 1.0 (revision 604). In general, we targeted and fixed trouble areas to improve overall application stability. This delivers an enhanced user experience. text/html 2021-06-29T14:30:53+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_1.2.0&rev=1624966253&do=diff What's new in version 1.2.0? PMA.core 1.2.0 is revision 883 of the PMA.core codebase. It follows PMA.core 1.1 (revision 784). General improvements in version 1.2.0: * LDAP support in the form of pass-through authentication (explicit PMA.core login still required) text/html 2021-06-29T14:30:12+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_1.2.1&rev=1624966212&do=diff What's new in version 1.2.1? PMA.core 1.2.1 is revision 906 of the PMA.core codebase. It follows PMA.core 1.2.0 (revision 883). General improvements * Remove limit in statistics * Improved memory management for MRXS slides * Inclusion of color correction data for MRXS slides text/html 2021-06-29T15:54:49+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_1.2.2&rev=1624971289&do=diff What's new in version 1.2.2? PMA.core 1.2.2 is revision 915 of the PMA.core codebase. It follows PMA.core 1.2.1 (revision 906). The software followed relatively quickly after 1.2.1, due to the fact that preparations for version 2.0.0 were already underway at this point. PMA.core version 1.2.2 then contains a number of urgent fixes that could not wait for text/html 2021-06-30T13:15:39+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_2.0.0&rev=1625048139&do=diff What's new in version 2.0.0? PMA.core 2.0.0 is revision 1803 of the PMA.core codebase. It follows PMA.core 1.2.2 (revision 915). It is a major revision, with many new features. Cloud storage support * Support for the S3 protocol, most known from Amazon AWS. The protocol is supported by many other vendors, including text/html 2022-02-03T17:34:18+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_2.0.1&rev=1643898858&do=diff What's new in version 2.0.1? PMA.core 2.0.1 is revision 2069 of the PMA.core codebase. It follows PMA.core 2.0.0 (revision 1803). It is a minor revision, with small refinements and bugfixes. File format improvements * Support for Bionavation SVS slides * Support for JPEG 2000 text/html 2022-03-28T13:26:38+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_2.0.2&rev=1648463198&do=diff What's new in version 2.0.2? PMA.core 2.0.2 is revision 2081 of the PMA.core codebase. It follows PMA.core 2.0.1 (revision 2069). It is a minor revision, with small refinements and bugfixes. General improvements * Enrich license metadata * Allow mounting points to be created even if PMA.core has no access to them text/html 2020-05-29T14:21:25+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_2.0&rev=1590751285&do=diff What's new in version 2.0? Added support for Amazon S3 like backing storage text/html 2022-07-13T13:13:40+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_3.0.0&rev=1657707220&do=diff What's new in version 3.0.0? PMA.core 3.0.0 is commit f47dcd30 of the PMA.core codebase. It follows PMA.core 2.0.2 (revision 2081). It is a major revision, with breaking changes, new functionality, small refinements and bug fixes. General improvements * Improved performance of listing root directories text/html 2023-01-23T11:11:46+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_3.0.1&rev=1674461506&do=diff What's new in version 3.0.1? PMA.core 3.0.1 is commit (be720dc8) of the PMA.core codebase. It follows PMA.core 3.0.0 (f47dcd301e). It is not a major revision, with small refinements and bug fixes. General improvements * DeleteDirectory API method now supports deleting recursively files, folders and subfolders text/html 2023-08-22T17:28:37+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=what_s_new_in_version_3.0.2&rev=1692714517&do=diff What's new in version 3.0.2? PMA.core 3.0.2 is commit (e3ee4dae) of the PMA.core codebase. It follows PMA.core 3.0.1 (be720dc8). It is a minor revision, with small refinements and bug fixes. General improvements * Added support for Olympus VSI slides using OME TIFF encoding. text/html 2022-02-24T16:39:29+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=who_should_read_this&rev=1645709969&do=diff Who should read this? Histotechnicians, pathologists, administrators and software engineers should read this user guide and use it for reference while using the system. This document is intended * for users (administrators) who need to know how to set up PMA.core, as well as text/html 2023-11-21T17:13:07+0300 Anonymous (anonymous@undisclosed.example.com) https://docs.pathomation.com/pma.core/3.0.2/doku.php?id=working_with_annotations&rev=1700575987&do=diff Working with annotations PMA.core supports three types of annotations: PMA.core annotations, native annotations, and 3rd party annotations. Annotation type Origin Format Read/Write Pathomation PMA.studio; SDK WKT Read/write Native Vendor-specific viewer; Pannoramic viewer; ImageScope