What's New - Neurolucida 360

Neurolucida 360 Version 2021.1.1

Released March 2021

New Features and Enhancements:

  • Added support for automatic z-alignment and using image names in the Image Montage tool
  • Improved puncta detection
  • Improved speed when tree segments are classified
  • Added ability to clip tracings on slices
  • Updated the Partition Contour window
  • Added more options for selecting markers, contours, or vessels with the new Freehand Selection tools
  • Updated tooltips that display when hovering on buttons and tools
  • Tracing with partial projection will automove the image through z
  • Updated the Illumination Correction tool
  • Updated how to access .blc files
  • Default image-save format is now .xml
  • Improved file support for the channel panel
  • Improved merge function for puncta editing

SPARC Users:

  • New Import 3D model tool to import and visualize generic organ scaffolds right in the 3D environment
  • Users can now keep the original color when linking to SciCrunch database
  • Added a LinkTerms exit button
  • Added ability to name sets with the SciCrunch term-list
  • Associate Link Terms to cell body contours
  • Increased the number of results from SciCrunch term-list searches
  • Associated terms are shown in the link terms window
  • Users can now load multiple term-lists into the term-verification window
  • New muscle fiber sugementation tool

Neurolucida 360 Version 2020.3.3

Released November 2020

New Features and Enhancements:

  • Added support for new AMD drivers
  • Additional Clean-Up functionality added to identify issues with varicosities
  • Decreased the time requires to detect puncta around the soma

Neurolucida 360 Version 2020.3.2

Released November 2020

New Features and Enhancements:

  • Added ability to select all dendrites, apical dendrites or axons in 3D environment
  • Reporting the thickness of a specific point in the 3D environment
  • Added progress bar for Clean-Up
  • Added support for additional OME-TIFF format

Neurolucida 360 Version 2020.3.1

Released October 2020

New Features and Enhancements:

  • Images and data files load noticeably faster than in previous releases
  • Neurolucida 360 software handles hundreds of thousands of data points simultaneously
  • Image adjustments are imediately displayed in both the 2D and 3D windows—without clicking any buttons
  • Multiple options to indicate how you want Neurolucida 360 software to handle and display your images
  • Drag and drop file opening is easier and more powerful with the new Image Opener window
    • Open all images in container files such as Leica ,lif and Zeiss ,czi formats
    • Choose to display in a grid, stack images, or display on top of each other without stacking
  • Puncta detection in the 3D environment replaces synapse detection present in previous releases
  • Puncta detection tool includes the option to use powerful new machine learning technology for accurate puncta detection
  • Color channel selection in the 3D environment via a new Channel panel enables you to select one or more color channels to view, hide, and associate data elements within your images
  • You can now associate traced structures with a specific color channel
  • New subvolume function in the 3D environment enables you to easily and systematically focus on portions of images/image stacks
  • Easier software authorization: Neurolucida 360 software autofills the online Authorization Request Form with information about your computer system
  • You can now classify segments of trees in tree-editing mode to facilitate later analysis using Neurolucida Explorer software
  • Research Resource Identifier (RRID) recorded in every .xml data file
  • Putative synapse markers work on all axon/dendrite pairs

Neurolucida 360 Version 2020.1.1

Released December 2019

New Features and Enhancements:

  • Image montage includes new method for 2D image alignment
  • Added ‘Select everything of this contour type’ option to the right-click menu
  • Add help access, improved statuses, icon, and login to Blackfynn access window
  • SPARC Vocabulary Services now launch when a data file or image file is opened, rather than when the software is started
  • Large Volume Reconstruction mode enhanced to adjust status warning

Issues Resolved:

  • Fixed inability to use Select All on varicosities with Show Current Section
  • Fixed display of branches in points mode, and varicosities with Show Current Section in some data files
  • Fixed crash when performing right click operations during contour editing
  • Fixed Pan to window center when detecting varicosities on nearest branch
  • Fixed inability to embed a scalebar
  • Fixed issue when changing contour type from circle contour 
  • Improved Batch Tracing user interface

Neurolucida 360 Version 2019.1.3

Released October 2019

New Features and Enhancements:

  • SPARC vocabulary services: Can use symbols in Subject ID Field
  • Added 'select everything of this contour type' option to the right-click menu

Issues Resolved:

  • Fixed image no longer visible when using Image Slice mode
  • Fixed cannot select spine palced manually in 2.5D window
  • Fixed 'close all' button doesn't clse Image Adjustment window, causing crash
  • Fixed SPARC Vocabulary Services: Search Contours bar doesn't let the user search for the first contour; list from previous session is displayed and FMA Id is not written to file
  • Fixed "Ï »¿"  characters are appended to the beginning of the first contour name upon uploading a .csv file; contour names hidden from Contour Settings window still displayed in Contour Selection window
  • Fixed Issues with configuring Blackfynn agent; after selecting ‘Remember me’ option when signing in for the first time, cannot sign in again

Neurolucida 360 Version 2019.1.2

Released July 2019

New Features and Enhancements

Detection, Tracing, and Classification:

  • Batch tracing is CZI supported.
  • Input text box to filtering slider under parameters added to cell detection workflow.

Misc:

  • Batch converter added (DAT to XML) — to access, type "convert" in the quick launch box.

Issues Resolved:

  • Fixed program can't skin somas traced as cell body contours.
  • Fixed branches that were deleted in 2D still being displayed in 3D.
  • Fixed closing the 3D window closes the entire program.
  • Fixed can't adjust contour thickness by typing a number.
  • Fixed using the slider to change the thickness then canceling the change, the cancel operation doesn't work.
  • Fixed movie playback functionality issues.
  • Fixed assicuated image doesn't open with data file after adjusting the histogram, but not saving the changes.
  • Fixed can scroll down to view all channels in image adjustment.
  • Fixed editing cell body contours may lead to a crash.
  • Fixed batch tracing may lead to a crash.

 

Neurolucida 360 Version 2019.1.1

Released January 2019

New Features and Enhancements

Detection, Tracing, and Classification:

  • End point of a trace changes colors when targeted when using user-guiding tracing system.
  • Automatic cell detection workflow added to speed up detection process.

Editing:

  • Nodes and points now distinguishable by color.
  • Added button to reset all selected contours/shells back to line mode display.

Scene and Display:

  • Completely redesigned preference panels with a handy search functionality.
  • Scalebar color and playment controls
  • New EMF detail slider.

Misc:

  • Display warning message when user attempts to change sections while moving to the next section.
  • Suppor for Huron jpeg files, definition for Huron file extension.
  • Support for Huron TIFF images.
  • LVR added to quick launch.
  • 3D contour drawing added.
  • 3D marker placement added.

Issues Resolved:

  • Fixed 3D automatic tracing: Could only be implemented once with multichannel image.
  • Fixed edit button in 3D didn't show any text; only possible to highlight/select one point at a time in Points editing.
  • Fixed hide Selection in Points mode only temporarily hid selected tree.
  • Fixed marquee selection no longer implemented after deleting node.
  • Fixed marquee selection notworking in Points mode and causing crash.
  • Fixed Marker panel being displayed instead of Contour panel when clicking Edit button.
  • Fixed changing contour appearance was not reflected in selected contour.
  • Fixed contour shell could not be built; the surface was not being updated when switching to Points mode; color change and transparency were not applied.
  • Fixed points mode crashed or didn't move the correct point for circle and freeform contours; couldn’t edit points in circular contour.
  • Fixed marker sizing UI issue. 
  • Fixed micrometers resizing didn’t work.
  • Fixed zooming didn’t work when using perspective projection
  • Fixed rounding error with partial projection thickness.
  • Fixed changes to the partial projection thickness and position could not be applied using the Enter key; crash when using marquee select.
  • Fixed the crash following synapse detection.
  • Fixed unable to select synapse after removing other synapses and changing color.
  • Fixed synapse transparency, user-guided tracing, and smoothing not implemented correctly.
  • Fixed detection failed in some CZI images; detection caused crash; detection failed with multichannel image.
  • Fixed batch tracing not working on some files.
  • Fixed 3D display update issue when point adjacent to node moved in 2D.
  • Fixed issue toggling between 2D continuous tracing and 3D user-guided tracing when connecting branches in 2D.
  • Fixed markers attached to 'soma contours' were not displayed in 3D; crash upon using CTRL-Z after tracing soma in 2D.
  • Fixed images being misaligned in exports; when tracing outside of the export area was still visible, open contours have sharp edges.
  • Fixed color by Branch Order 2D didn't reflect 3D.
  • Fixed  2D and 3D thicknesses not consistent after changing thickness; when moving the point near a node in 2D, the surface in 3D wasn't built correctly.
  • Fixed sometimes incorrect scaling resulting from dragging multiple image files into the application.
  • Fixed various problems processing large jpeg2000 files.

Neurolucida 360 Version 2018.1.1

Released May 2018

New Features and Enhancements

Detection, Tracing, and Classification:

  • Display all trees as centerline while the tree being traced is displayed with the actual thickness.
  • Voxels in a single location cannot be identified as both a varicosity and a spine.
  • Varicosity detection is restricted to the varicosities whole center is located at least one radius away from the start or the end of a branch.
  • Improved automatic tracing in image volumes with numerous Z planes.
  • Reconstruct from a very large image volume and define subvolumes and trace in 3D.

Scene and Display:

  • Movie production has been redesigned and expanded functionality.

Misc:

  • Apply filters (Golgi, in vivo, closing, projection) to multiple images without opening them.
  • Function toggles between zooming and focusing depending on cursor location.

Issues Resolved:

  • Fixed crash after detaching several trees using the marquee method.
  • Fixed single point branches not being able to be deleted/using marquee to select and delete two-point branches generated by a detach operation leading to crash.
  • Fixed crash after tree deletion then image rotation.
  • Fixed trees not being recognized after being selected in connect mode.
  • Fixed potential crash resulting from tracing one image and modifying Z in 2.5 window, then loading a secon image and starting to trace in 3D.
  • Fixed potential crash when deleting a point in 2D after deleting another point in 3D.
  • Fixed Axial smear option slowing down detection for large trees.
  • Fixed nothing on axons being detected.
  • Fixed two nodes being displayed as one.
  • Fixed crash when selecting partial projection after connecting two branches.
  • Fixed crash when selecting new color for bounding box.

Neurolucida 360 Version 2017.01.4

Released December 2017 

Issues Resolved:

  • Fixed "Align tracing" was not immediately reflected in 3D environment.
  • Fixed selecting "Cleanup" functionality when there is no problem to identify caused the 3D environment window to go blank.
  • Fixed texture wasn't applied properly when editing variconsities.
  • Fixed "Partial projection"was turned back on after using "image sync with 2D"
  • Fixed using "image sync with 2D" caused a crash with certain image adjustments.
  • Fixed scale bar didn't display properly in Quad View
  • Fixed some images were not rendered in 3D due to inadequate graphic card settings.
  • Fixed could't select a marker by clicking it.
  • Fixed "Select by selection" functionality was only availble after drawing a new contour.
  • Fixed using the ESC key to exit marker selection caused crash.
  • Fixed issues related to CZI and VSI files.
  • Fixed main window didnt restore to full size when returning to it from the task bar.
  • Fixed ending types were not correctly applied.

Neurolucida 360 Version 2017.01.3

Released October 2017

New Features and Enhancments

Detection, Tracing, and Classification:

  • Spine detection range increased from 15 to 20 micrometers.
  • Spine detector can use voxels past end of dendrite for interactive detection.
  • Surface area and otehr spine metrics can be calculated from outside the spine detector.

Issues Resolved:

  • Now preventing Axial Smear Model from flattening dendrites (occasionally, thicker dendrites were flattened in the axial direction during spine detection as an artifact of the model. To solve this we now guard against smear values lesser than 1).
  • 3D soma display now updated when shrinkage or transformation is applied.
  • 3D tracings no longer disappear when Cleanup tool doesn't identify any issue.
  • Select all button no longer selects all objects when no object type is checked.
  • Selecting all objects in files with synapses but no markers no longer results in a crash.
  • Post processing is now implemented on all trees.
  • Hardware settings no longer displayed since they are not relevant.
  • CZI files with multiple regions and different resolution levels now loaded properly.
  • Image scaling.

Neurolucida 360 Version 2017.01.2

Released September 2017

New Features and Enhancements

Detection, Tracing, and Classification:

  • In the trace ribbon, click Automatic>Batch Trace to generate the automatic reconstruction of somas, trees, and spines over multiple images.

Misc:

  • Marker deletion improved, more stable, faster with marker summary updated.
  • Contour functionality in 3D environment improved.

Issues Resolved:

  • Adjustment of the circular cursor now possible below 1 micrometer in diameter.

 

 

Neurolucida 360 Version 2017.01.1

Released April 2017

New Feautures and Enhancements 

Detection, Tracing, and Classification:

  • Varicosities detection added (available with Neurolucida 360 Studio).
  • "Clear last" soma button added.
  • Synapse detection now available for axons, in addition to dendrites and apical dendrites.
  • Spine backbone length is reported by default.

Editing:

  • Cleanup tool added to identify and remove tree framents quickly after automatic tracing.
  • Marker sizing added to Edit Markers panel. Similar to 2D sizing (pixels, microns. or intrinsic).

Scene and Display:

  • 3D scale bar added.
  • 360 window renamed 3D environment.
  • Redesigned user interface with new icons.
  • When selecting an option and then selecting a different option, the display is updated.
  • Completely revamped user interface: ribbon bars replaced toolbars and menus.
  • Redesigned marker toolbar.

Misc:

  • Open data file in Neurolucida Exporer from the 3D environment with one click.
  • Objects can be grouped for analysis in Neurolucida Explorer.
  • Added option to save scaling information with image file and convert to .jpx format.
  • New version notification window displayed when opening program.
  • Apotome CZI, ND2, Calibar ID scanner, Bacus, Janelia, VSI, LSM files>4GB, tiled LSM, and multi channeled tiled LSM now supported.
  • Support for 4K monitors and Windows 10.
  • Support for saving and opening data files from Biolucida servers.
  • Improved handling of very large images.
  • Alert is displayed when dongle is not plugged in.
  • Context-sensitive help now availble for users without internet access.

Issues Resolved:

  • You no longer need to close and re-open the 3D window to display markers placed in 2D .
  • Changes made to marker colors or visibility in 3D are now reflected in the 2D markers.
  • Selecting and changing transparency for a single marker no longer results in changed transparency for all markers.
  • Fixed marquee selection in Point editing mode. 
  • In Edit Contours, smoothness filter enabled when creating a contour shell from at least 3 contours.
  • Undo move for contours.
  • Setting origin no longer changes the tree type from Axon to Dendrite
  • Fixed issue where deleted point appeared again after using under to cancel moving another point.
  • Now works in all views when using Quad View (instead of XY only).
  • Somas now updated in 3D after using "Move Images and Tracing". 
  • When hiding one soma, then another, clicking "show all" now shows all the hidden somas. 
  • Soma contours from different cells no longer linked as one single cell in 3D.
  • When tracing a cell body in 2D with the 3D window open, the system no longer crashes.
  • Right-clicking first or last point of an arrow no longer results in crash.
  • No more flickering in Multichannel dialog.
  • Dialog layouts are now displayed correctly when using a language that is read right to left.
  • Tif image files can now be updated with new color maps or with image processing.
  • Removed a number of error messages that can occur when adjusting during image stack auto-loading of a data file.
  • Fixed two rare crashes that could occur while adjusting on a currently unloading image stack.