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KNOSSOS Changelog

What's new in KNOSSOS 5.1

Feb 5, 2019
  • Bug Fixes:
  • Merging trees now correctly merges their meshes, too.
  • The display of translucent meshes has been improved.
  • Segmentation bucket fill: Buggy behavior at vp and movement boundaries have been fixed. Performance of the bucket fill has been improved.
  • Some issues when filtering in the annotation tables have also been fixed.
  • New Features:
  • Annotation:
  • Mesh slice in orthogonal viewports. Previously the mesh was only visible in the 3D view.
  • Mesh transparency can be adjusted.
  • Skeleton and Segmentation table entries are now copyable to clipboard.
  • Skeleton nodes table: A new context menu entry lets you select all trees that contain selected nodes.
  • Segmentation: Rendering of borders of segmentation objects can be toggled off now.
  • Settings:
  • Settings per annotation file: Just add a settings.ini to your .k.zip.
  • Beginning with this version, settings are maintained and compatible between different versions.
  • Datasets:
  • Support for new NeuroData Store url naming scheme (previous scheme still works): /ocp/ca/ ↦ /nd/sd
  • We added a new default dataset
  • Other:
  • Cheatsheet: An informative side panel with an overview of the active work mode including shortcuts and links to related settings.
  • Snapshot preview: Let’s you copy to clipboard, no need to save to file.
  • There’s now a progress bar indicating network activity.

New in KNOSSOS 5.0.1 (Feb 5, 2019)

  • Enhancements:
  • Improved performance of operations on large number of trees/nodes
  • Keep orientation when switching between equivalent datasets
  • Adapted scale bar length to display »rounder« values
  • Added base grid for 3D viewport’s boundary box
  • Fixes:
  • Node view selection only worked in one work mode
  • Corrected task management display
  • Fixed arbitrary viewport regression (viewport sometimes went mostly black)
  • Fixed zoom-in shortcuts

New in KNOSSOS 5 (Feb 5, 2019)

  • Other improvements:
  • KNOSSOS does not consume as much computing power anymore while running in the
  • background.
  • Features:
  • Dataset:
  • The dataset loading mechanism was updated to support a wider range of dataset configurations, including
  • local jpeg-compressed raw datasets (additionally to remote ones)
  • customizable dataset cube sizes
  • various dataset backends. For example a dataset url containing “/ocp/ca/” will be interpreted as an open connectome dataset.
  • Mesh:
  • It is now possible to load triangle meshes into KNOSSOS. Meshes are a set of vertices, colors and indices. In KNOSSOS they are associated to one skeleton tree and are displayed inside the 3D viewport.
  • Simply insert a mesh file (.ply) into a KNOSSOS annotation file (.k.zip) and it will be loaded with it.
  • Visit our wiki to read about the exact file format.
  • Inside KNOSSOS you can jump to specific areas of interest: Just click on the mesh location and press S.
  • Skeletonization:
  • Trees are now traversed along the edges (depth-first-search) with X and Shift+X (previously, traversal order was defined by node ID).
  • You can now enable anti-aliasing for a smoother skeleton visualization.
  • Node comments can be displayed directly inside viewports. This should improve your orientation.
  • Synapses feature:
  • For neural annotations you can now create synapses with a synaptic cleft as
  • Well as pre- and postsynapse:
  • Simply perform your ordinary skeletonization.
  • On encountering a synapse, end the current tree with Shift+C. The last placed node is marked as pre-synapse.
  • Now annotate the synaptic cleft by placing nodes along it as usual. When you are finished, press C to end the cleft.
  • The next placed node will be marked as post-synapse.
  • Properties feature:
  • Until now additional information about trees and nodes had to be crammed into the respective object’s comment section. This became unreadable and hard to parse very quickly.
  • So we introduced customizable and visualizable properties. Properties are either simple text or textual or numerical key value pairs.
  • Numerical node properties can be highlighted inside the viewports: You can choose to scale radius by property value or to map property value to color map value, or both.
  • Segmentation:
  • You can now perform bucket fills, with the viewport being its maximum scope (middle mouse button)
  • Segmentation operations are now possible in all magnifications instead of only in mag 1.
  • The form of the segmentation brush is now aligned with the image pixels.
  • The color of segmentation objects can be changed.
  • Annotation in general:
  • You can use the dropdown in the toolbar to quickly switch between different
  • work modes, e.g.:
  • “Tracing Advanced“: More complex tracing operations such as unlinked
  • nodes or multiple trees have been moved into this separate work mode,
  • so that ordinary tracing has become simpler and less error-prone.
  • “Merge Tracing”: In this mode skeletonization and segmentation are
  • performed simultaneously: Place nodes on segmentation sub-objects to
  • automatically merge them together. The result will be a classical
  • skeletonization in which each tree corresponds to one merged
  • segmentation object.
  • “Review”: A segmentation proof-reading mode in which painting and
  • merging are disabled to prevent accidental modifications.
  • Skeletonization serves as review annotation.
  • A movement area can be defined to restrict your work to a specific location
  • of interest. Everything outside this area is darkened to an adjustable
  • degree and cannot be modified.
  • Spacebar hide: The viewport is often cluttered with nodes, edges,
  • segmentation overlay and viewport tools. Hold the spacebar and everything
  • except the raw dataset will be hidden for this duration.
  • Python Plugin Manager:
  • KNOSSOS now has a plugin manager, allowing you to write and share plugins written in Python in an online repository.
  • For example you can write custom GUI elements, create annotations programmatically or utilize your own algorithms. The idea is to customize KNOSSOS and make it fit your unique workflows.
  • As a starting point and reference we have a set of plugins available at https://github.com/knossos-project/knossos-plugins.
  • The Manager can be found under the “Scripting” menu entry.
  • User Interface:
  • In the Annotation widget we replaced the previous skeleton view that caused performance problems for large skeletons. The new table also supports sorting.
  • Skeleton as well as segmentation tables consume less space. There is only
  • one segmentation table, but if overlapping objects are selected, they are
  • shown in an extra table.
  • We moved various options into preferences widget to reduce the number of
  • floating windows in KNOSSOS.
  • When loading a dataset, you can specify a field of view for the viewports.
  • We tried to make all shortcuts visible in the user interface.
  • Comment shortcuts have moved from the F keys to the number keys.
  • Zoom:
  • The zoom interface now supports dynamic switching between magnifications.
  • A value of 100% represent the highest magnification.
  • In the 3D viewport KNOSSOS now zooms in at the cursor position. To inspect
  • something closer, simply let the mouse cursor hover over it while zooming.
  • In conformance with most other user interfaces, Ctrl++, Ctrl+- and
  • Ctrl+0 are now the shortcuts for zooming in, out or to reset zoom.
  • Viewports:
  • You can now take viewport snapshots of varying resolutions. The snapshots can be configured to decide what should be visible in them, e.g. only raw data, segmentation, skeletonization etc.
  • Viewports can be undocked and positioned independently of the KNOSSOS window. Especially, multi-screen workplaces might find it useful to place a fullscreen viewport onto one screen.
  • A scalebar in every viewport shows the dataset’s physical dimensions.
  • The 3D viewport now supports wiggle stereoscopy, just hold W. Wiggle stereoscopy is a computer graphics method to make the 3-D nature of structures better recognizable.
  • Inside the plane viewports KNOSSOS now shows information about what’s underneath your mouse cursor:
  • The position inside the dataset (shown in the lower left corner)
  • The segmentation object id at that position (shown below the segmentation table in the annotation widget)
  • A fourth viewport with arbitrary orientation can be turned on. One of the purposes of an arbitrary view is to automatically orient itself orthogonally to the skeleton while tracing. This feature is still experimental.

New in KNOSSOS 4.1.2 (Feb 5, 2019)

  • Noteworthy Changes:
  • merging trees resulted in a crash
  • range delta and bias did not work properly
  • more intuitive node selection
  • performance improvements
  • internal and visual improvements to the Heidelbrain integration

New in KNOSSOS 4.1.1 (Feb 5, 2019)

  • Fixed issues:
  • Segmentation overlay is disabled by default (less resource consumption).
  • Extracting a connected component as a new tree works again.
  • Jumping to next node now respects the comment filter from the annotation window.
  • Lower idle cpu usage
  • No broken movement after loading a new dataset while in magnification > 1
  • The 3D segmentation brush is now visible.
  • Dataset loading widget is more intuitive.
  • File handling on Mac
  • Node selection on MacBook Retina

New in KNOSSOS 4.1 (Feb 5, 2019)

  • Bug fixes:
  • Annotation time will not reduce anymore when running KNOSSOS too long.
  • Resolved several crash conditions.
  • KNOSSOS now works with node IDs up to 4e9.
  • Node selection difficulties fixed.
  • Comment modification working properly again.
  • Changes:
  • Skeleton files (.nml-files) will still be supported continuously, but the new KNOSSOS annotation file (.k.zip) is now the default file type.
  • The former 'Comment Settings' Window has been moved to the 'Comments' tab in the Annotation Window. You can define comment shortcuts from F1 - F10.
  • The table row size within the Annotation Window has been reduced to display more rows.
  • The annotation time is now displayed at the bottom right corner.
  • Arbitrary viewport orientation now needs to be enabled at 'Windows' -> 'Viewport Settings' -> 'Slice Plane Viewports'.
  • Both tabs for the heidelbrain integration have been merged.
  • Features:
  • Dataset:
  • A new KNOSSOS cuber in Python is now available. It allows easy conversion from image stacks to KNOSSOS datasets. Currently supported file formats: tif, png and jpeg.
  • KNOSSOS now remembers your last used datasets and displays identifying information about them.
  • Datasets can now be loaded by specifying a .conf file. Specifying a dataset folder is still supported.
  • Two streaming datasets of the mouse retina are now shipped with KNOSSOS.
  • Changing the Supercube edge size does not require a restart anymore.
  • Segmentation:
  • The segmentation feature allows to annotate the volume of neurons where skeletonization only reconstructs morphology and connectivity.
  • Activate this feature at 'Edit Skeleton' -> 'Segmentation Mode'. The settings for it can be found at 'Windows' -> 'Annotation Window' -> 'Segmentation'.
  • The Brush tool is used to perform original segmentation or to correct existing segmentations.
  • Edited cubes can be saved and loaded as part of the annotation file.
  • The Merge tool is used to connect or disconnect existing 64bit int segmentation objects.
  • The result can be saved and loaded as a ›mergelist‹ as part of the annotation file.
  • We support segmentation data in the form of raw 64-bit matrices optionally compressed with google-snappy and zip.
  • Skeletonization:
  • The new Simple Tracing Mode prevents annotation mistakes through reduced functionality.
  • Turned-off Features are: creating a new tree, placing unconnected nodes and creating cycles within the skeleton.
  • You can deactivate Simple Tracing Mode at 'Edit Skeleton'.
  • KNOSSOS now supports >5e6 nodes (loading, saving, and parallel visualization of up to 500k nodes).
  • Node comments can be displayed in the orthogonal viewports by enabling 'show node comments' at 'Windows' -> 'Viewport Settings' -> 'Slice Plane Viewports'.
  • Python plugin interface (experimental):
  • KNOSSOS is now fully scriptable through PythonQT and additional functionality can be added with pure Python code.
  • A Python plugin repository will be available on the KNOSSOS website soon.

New in KNOSSOS 4.0.1 (Feb 5, 2019)

  • press 5 to temporarily display the uncompressed data of compressed remote dataset. Current compression is visible in the Zoom and Multiresolution widget
  • fixed a major performance problem on systems, where vsync was not disabled
  • downloaded files from remote datasets are now deleted after loading