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PathcoreFlow Release Notes

PathcoreFlow™ Release Notes

v4.0 (2024-12-16)

In PathcoreFlow v4.0, we've unveiled an all new Image Settings panel for the Viewer. It includes improved controls for adjusting how images are displayed, the ability to save and share these settings with your team, and a fully-featured histogram, among other features that make working with multispectral and fluorescence image formats easier and more enjoyable.

New Features

Interactive Image Histograms

High fidelity histograms, derived from the highest resolution image layer, are available in the image settings tab of the Viewer (currently limited to multiplex (non-RGB) images). These histograms are performant and interactive, and allow users to precisely control the rendering properties of channels individually and in groups.

More details on how to use this powerful new feature can be found in the Histogram section of the User Manual.

Save and Share Image Settings

Easily save render settings and share them with team members, or define preferred rendering settings for others to use. These capabilities streamline collaborative workflows by allowing multiple users to look at the biology with the same lens, via a centralized cloud-based image management software.

See Sharing Settings With Your Team for more details.

Transfer Image Settings to Other Images

Built-in functionality allows users to easily transfer image settings across images and studies. Transferring image settings across images works best when images have been imaged with the same protocol (i.e. when number of channels and channel names are the same).

More information about how to manage Image Settings can be found in the User Manual.

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.

The Image Settings panel also adds the ability to report the intensity values of each band in a multispectral image.

Find out more in Basic Controls and Pixel Value Reporting

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

SAML Integration for Upload Client

  • This release includes an update to the SAML integration which adds support for the Pathcore Upload Client. This will provide more authentication options and improved security for the Upload Client.
  • Note: these improvements are required for the upcoming Pathcore Upload Client release (v2.2). And so, all future releases of the Upload Client will only be compatible with PathcoreFlow v4.0 and newer.

Fixed in this Release

Viewer Fixes

  • 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 legacy 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
  • Fixed a bug that could prevent a user from being able to toggle the display of annotations and scale bar in a Figure

Repository Fixes

  • Fixed an issue where files used to cache certain image data by PathcoreFlow might be included when downloading a multi-file image
  • Fixed an error that would occur when a user saved changes to an item's metadata with the Activities tab open

Image Format Fixes

  • 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 PathcoreFlow

API Fixes

  • 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

Notes for On-Premise Customers

  • There is an update to the Docker Compose configuration with this release. Contact Pathcore Support for assistance with this change.