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PathcoreScholar Release Notes

PathcoreScholar™ Release Notes

v2.1 (2025-02-24)

This release of PathcoreScholar includes several improvements such as faster download speeds and the ability to toggle cursor tracking in the Viewer. Additionally, many bugs have been fixed to enhance the usability, stability, and security of the software.

New Features

Status Icons

The Repository now displays a status icon next to an item's name if there is something notable about that item. For example, if there are Share Links, an image is missing, or an upload is incomplete. Hovering over the icon provides more detail.

Additionally, there is a new System Field: Status. This field currently has three possible values - "Available", "Not Available", or "Missing" - and can be used in search queries. This new field replaces the "Availability" column in folder listings, which has been removed.

Unrestricted and Lightning Fast Downloads

Greatly improved download experience enables partial or complete export of the Repository. Improvements include faster download speeds, greatly reduced archive generation time, elimination of the 100GB size restriction (now unlimited), and other improvements such as the ability to pause and resume interrupted downloads.

To review all of the options available when exporting from the Repository, see Downloading in the User Manual.

Cursor Tracking Reports X/Y Coordinates

A new cursor tracking feature in the Viewer’s toolbar will report the X/Y location of the cursor relative to the full resolution pixel grid, when enabled. It also reports the RGB (red, green, and blue) values for brightfield images.

Find out more in Basic Controls.

Service Accounts

A new Service Account user type, which uses token-based authentication is available to support more robust integrations and automations in the future. Service accounts are not yet accessible in the UI.

Improvements

Viewer Improvements

  • Freehand annotations now support length and area values (where possible)
  • Multi-spectral QPTIFF images which include biomarker metadata for individual channels now show that information in the Image Settings dialog

Repository Improvements

  • Accuracy of the "storage used" value has been improved
  • The System Field "Parent Name" has been renamed to "Location"
  • The folder side bar on mobile devices can now be toggled on and off rather than being displayed below the folder content
  • Folder pagination controls on mobile devices are more compact and easier to use
  • Downloaded CSV exports now include URL links to each item
  • The context menu now has a "Copy URL" option so users can paste a direct link to the item from their clipboard
  • Folders now have the same read/unread indicators as files

Image Format Improvements

  • PathcoreScholar now supports 16-bit QPTIFF images
  • Added support for the Lunaphore variant of OME-TIFF
  • When a user creates a Share Link, "Anonymize data" defaults to on if that user does not have access to PHI, and cannot be toggled off

Settings Improvements

  • The direction of column sort markers in User settings is now consistent with the rest of the product

API Improvements

  • Added an optional verify stage to the multi-file upload API which compares server and client file fingerprints to ensure reliable data transmission
  • Added an API for calculating the properties of a selection of nodes and their children, including estimated size and list of node types found
  • Added an API for listing Share Links associated with a selection of nodes and their children

Other Improvements

  • Our Help Center has been enhanced by the addition of a Frequently Asked Questions page
  • Various other changes and improvements to improve performance, reliability, and assist with future feature updates

Fixed in this Release

Rich Text Editor Fixes

  • Fixed an issue where an image dragged onto a page that was then interrupted during upload could cause the page to always show the "Something went wrong" error thereafter

Viewer Fixes

  • The blue border of the active image is no longer clipped
  • Fixed a bug that prevented ICC profiles from being applied properly
  • Deleting an image from the Browse Folder panel no longer results in an endless loading icon
  • Fixed a problem where creating a Share Link from within the Viewer could sometimes result in a "Something went wrong" error screen
  • Fixed a bug where the Overview panel would disappear if the word "Overview" was tapped in mobile view
  • Fixed a bug that would sometimes set the magnification of an image to the wrong value when manually typing in the desired magnification value
  • Fixed a bug which caused the rotation tool to stutter or jump around
  • Fixed a bug which could cause images to be locked to a specific rotation value
  • Removed the limit on number of annotations which can be displayed
  • Viewer URLS now properly support negative numbers for the position parameters
  • Fixed a bug where the heatmap was not updated for all sub-images of an image if it has multiple sub-images
  • Fixed a problem where a horizontal scroll bar could appear in the Viewer when using the "Fit" aspect ratio
  • Fixed an issue where freehand annotation drawing could get stuck on
  • In certain cases, drawing a freehand annotation could disappear when the mouse is released at the end of drawing
  • Rapidly rotating an image could result in the rotation value being locked. This has been fixed
  • Fluorescence images with Lookup Transforms no longer display incorrectly if a Gamma change is applied
  • Fixed a bug where the entire page was re-rendered when anything inside of a Viewer panel changed
  • Fixed a bug with the "Auto Scale" button in the Image Settings dialog. It can once again be used to automatically set the black and white points for all image channels
  • Fixed an issue where some annotations or overlays shifted position with respect to an MRXS image as the zoom level changed
  • Fixed a bug that could make the keyboard shortcuts for next/previous image behave unpredictably
  • Fixed a bug that would cause an error when a Share Link user tried to change an overlay's composite operation

Repository Fixes

  • Fixed a bug that caused all items in the Summary page list view to be unclickable
  • The quick search field is no longer cleared if a user opens an image in the Viewer then uses the back button in their browser to return to the Repository
  • Fixed a bug where deleting a folder with many items would cause it to rapidly disappear and reappear in the folder listing
  • Fixed a bug where an image with a large difference between width and height could fail to load a thumbnail
  • Now users are able to rename a folder to a name with a single character, instead of requiring a minimum of 2 characters
  • Copying an item now adds "Copy of" to the start of the new name and updates the timestamps so it is easier to distinguish the copied file
  • Fixed an issue where some pop up menus could get cut off in smaller window sizes
  • Previously, adding many columns when viewing a folder could cause the right side bar to get cut off. This has been fixed
  • Sorting a folder by file size no longer results in an "unknown error" message
  • Fixed a bug which could allow a user without the "View Protected Health Information" permission to download a single-file image
  • Fixed an issue where files used to cache certain image data by PathcoreScholar might be included when downloading a multi-file image

Image Format Fixes

  • Fixed a bug which could lead to a service disruption when processing a corrupt or truncated VSI image
  • Fixed a bug which could lead to service degradation when attempting to attach a full-size, non-pyramidal overlay (such as a PNG) to a WSI
  • Fixed an issue with certain Zeiss CZI images failing type detection because an optional field was being treated as required
  • Image server could stall rendering certain thumbnails because a maximum area check was inconsistently applied
  • Certain SVS images would not report having an overview image when in fact they did. This has been fixed
  • Fixed an issue with TIFF images that do not specify rows per strip
  • Fixed an issue with OME-TIFF images that do not specify plane count
  • Fixed a bug which could lead to a service disruption when processing corrupt JPEG2000 compressed SVS images
  • Removed the subfile type checking for OME-TIFF images, as it is inconsistently set by scanners
  • Fixed an issue where 16-bit MRXS files were being downscaled to 8-bits
  • Fixed a bug which could lead to a service disruption when processing certain corrupt VSI images
  • Fixed an issue that prevented OME-TIFF images from RareCyte Orion devices from working in PathcoreScholar
  • Security restrictions prevented Share Links from being embedded in local HTML files. This has been addressed for browsers that support it

Search Fixes

  • Fixed a bug where reopening the "Select field" dropdown menu after initial selection would highlight all of the available options

Settings Fixes

  • The next/previous controls in the user list might not function correctly. This has been fixed
  • Fixed a bug that could cause a user's password to erroneously be reset when they filled out the "Change Password" dialog but clicked on the "Cancel" button

API Fixes

  • Fixed a bug where a multi-frame request would only return a single frame
  • Fixed a bug that could cause an internal server error (HTTP 500) when attempting to create a Share Link with permission_restrictions defined
  • Retrieving a signature for a user without one set now correctly returns a 404 status code instead of a 500 error
  • Fixed an issue where uploading an image via the API would fail if encoded as multipart/form-data
  • Previously, application access tokens were stored as-is in the database. They have been replaced
  • The custom field and custom field set API endpoints now return an HTTP 409 response when attempting to create a new entry with an existing name, instead of an HTTP 500 internal server error
  • Fixed an issue where files uploaded via the multi-file API would always report a file size of 0 bytes
  • Fixed an issue where the multi-file upload verification endpoint could sometimes fail instead of gracefully handling an unexpected state
  • API endpoints that can return cached metadata (i.e., "shadow files") now default to returning cached data rather than relying on an API parameter to control the behavior

Other Fixes

  • ZIP files using compression mode 9 (Deflate64) are now properly supported
    • This was primarily a problem for ZIP files greater than 4 GB created in Windows Explorer
  • Fixed CSV export of annotations for images with different pixel scales in the x and y directions
  • Attempting to change a Team name to something longer than 256 characters now displays an appropriate error message
  • Fixed a bug where any small annotations (which have too few points to calculate area or perimeter) would cause CSV export to fail
  • Other bug fixes and UI improvements