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PathcoreFlow Release Notes

PathcoreFlow™ Release Notes

v3.1 (2023-03-08)

Version 3.1 includes exciting improvements in the Viewer such as the ability for digital zoom and an auto scale feature for multi-spectral images. In addition to these, we have made a number of improvements to enhance user experience and fixed many bugs. More details below.

New Features

Auto Scale

An "Auto Scale" control has been added to the Viewer’s image settings dialog. This feature automatically configures the black and white points of multi-spectral images based on the dynamic range of each channel. The Auto Scale button can be used to improve contrast and establish baseline values for the black and white points quickly.

The auto scale feature is accessible from the Image Settings panel of the Viewer in PathcoreFlow v3.1.

Digital Zoom

Digitally zoom up to 400%.

You can now zoom images beyond their native resolution up to 400%. For example, if an image has a maximum magnification of 20x, it can be scaled up to 80x and even more when in a synchronized multi-panel configuration via the Split View feature.

Additionally, the current magnification is now always visible in the bottom left corner of an image in the Viewer, even when it’s not the active image, in a Split View configuration. When digital zoom is enabled for an image, a blue border and a "Digital Zoom" indicator is shown adjacent to the current magnification to unambiguously inform viewers.

Improvements

A number of enhancements have been made to improve the usability of the software based on customer suggestions and feedback.

Viewer Improvements

  • The Viewer rotation tool now accepts values with a precision of a 10th of a degree (e.g. 43.7°), rather than only accepting integer values
  • The current magnification value in the Viewer has been moved to the bottom-left corner and clearly differentiates digital zoom values
  • Added support for estimating the magnification of OME TIFF images from pixel size when the file does not provide a magnification value

Repository Improvements

  • Long folder breadcrumbs in the Repository are now collapsed into an ellipsis, to prevent it from taking up too much space when navigating deep folder structures. You can click on the ellipsis to get the full list, so you can still quickly jump to any folder in the current path
  • The Move Item and Copy Item dialog boxes have been updated to show the full breadcrumb of the selected folder

Other Improvements

  • The search bar in the users tab is sensitive to all columns of the users table, not just the user’s name
  • Exporting metadata as CSV now includes the file size in bytes
  • The files in the Unsorted Uploads page can be sorted and organized using the same tabular capabilities as in the Repository

Fixed in this Release

In this release, we have implemented the following bug fixes and UI improvements to address customer suggestions and feedback.

Viewer Fixes

  • The Polygon annotation tool has had several fixes:
    • The Ctrl + Z keyboard shortcut now undoes only one point instead of all points
    • Panning with the Arrow key panning works correctly while drawing
    • Zooming with the mouse wheel works correctly while drawing
  • Corrected the keyboard shortcut behavior when viewing multiple images in Split View
  • Corrected a behavior that sometimes led to the Viewer forgetting which sub-images have been hidden upon refresh
  • Fixed a problem where Figures with multiple images in Split View would sometimes not save the position and/or magnification for images in a synchronized set
  • Dragging an image from the Browse Folder panel into a Figure will now correctly assign the image name as the Label text, not the ID
  • Navigating to the Uploads folder from the Viewer now works as expected
  • Fixed a problem where very wide snapshots would sometimes render as blurry in the information panel

Download Figure Fixes

  • It is no longer possible to create a Figure with a scale bar which is too large to display
  • Downloading a Figure in "Fit" cell aspect ratio should now render with the aspect ratio in the user's preview window, instead of a square (1:1)

Image Format Fixes

  • Fixed a problem with some ND2 images that could cause the Viewer to fail to load
  • CZI images with sub-images that overlap no longer obscure each other

Repository Fixes

  • Sorting a folder by Size in the Repository no longer shows an empty folder
  • The Move Item dialog box now prevents a user from moving a folder under itself, and provides a warning explaining why it is not a valid destination
  • Deleting a file or folder from the Repository no longer causes the item to "flicker" in the list of items while the delete is in progress
  • Corrected problem where attempting to open a Figure which had been created using the "Save As..." dialog would only display a loading animation
  • Fixed a problem where the Move Item dialog box would sometimes not load all available folders

Search Fixes

  • Fixed an error that could occur when searching for a custom field with a number type
  • Corrected the problem that caused some search results of the user list in Settings to be missing.
  • Corrected the behavior when a search term includes a double quote or other special character. Search now returns results matching those characters

Visiopharm Integration Fixes

  • Fixed problem where Visiopharm batch processing via the PathcoreFlow integration plugin would sometimes fail. This fix requires Visiopharm version 2022.09.4 or later
  • Corrected the calculation used to determine the center of QPTIFF images, which fixes a zoom problem with this image format when opened in Visiopharm from PathcoreFlow
  • Fixed problem where annotations nested within a larger annotation failed to import into Visiopharm

Other Fixes

  • Fixed an error that may occur when attempting to bulk import metadata from a CSV file as a limited user (rather than an administrator).
  • Fixed an error that sometimes occurred when a non-administrator user attempted to move an item in the Repository
  • Other bug fixes and UI improvements