Updates history

0.4.0

Major update: time tracking addition

• added a new Tracking panel to track curves over time (appears only with timelapse datasets);
• added a button to align ROI end-to-end direction in the same group;
• added optional user-provided intensity threshold termination of one click tracing;
• intensity measurements outside of the volume are now ignored, rather than padded with zeros;
• added ROI's point size and line thickness to the measurements Results table;
• fixed initial snapping of tracing point to the largest local saliency value (now inside the volume);
• fixed concurrency render problem for one click tracing mode ROI visualization, any render type is possible now;
• added a shortcut to delete selected ROI using "Delete" key;
• added macro function to load ROIs;
• added macro function to export straightened ROIs;
• added macro function to close BigTrace;
• added a button to store default settings for the undefined Group;
• added a button to merge Groups in Groups Manager;
• storage of active ROI colors is enabled;
• moved actions to a separate class;
• switched to bvv-playground v.0.2.1, so now can use LUTs to display volume data;
• fixed a bug of wrong image calibration data in the Export ROI box function;
• fixed a bug with a IJ.prefs storage of extended click volume around the ROI parameter;
• changed parallelization for TraceBox a bit;
• updated some generics handling;

0.3.9

• new option: a user can select the output axis along the curve in the output of Straighten command;
• there is an option now to clip the volume around ROI when double-clicking on it in the ROI list/manager;
• added feature to continue one click tracing of the selected LineTrace ROI the F shortcut;
• for one click tracing mode ROI visualization is always performed in WIRE mode now, since somehow SURFACE takes too much time to compute and sometimes breaks the plugin (need to figure out why, but most probably it is a concurrency issue);
• added feature to extend LineTrace ROI with a straight segment (shortcut R) in one click tracing mode;
• after running the initial one click tracing, ROI is automatically deselected;
• fixed a bug with vertex location after clicking in volumetric rendering mode of multichannel data;
• changed to bvv-playground distribution via scijava maven with the help from @ctrueden;
• updated and cleaned up pom a bit.

0.3.8

• added possibility to extract bounding box around ROI.

0.3.7

• vertex/click point selection in Volumetric rendering mode is now different (compared to Max Intensity) and depends on opacity/rendering settings for the dataset. It selects the closest to the viewer point with opaqueness ~1 (and looks locally for the maximum intensity);
• related to this: new, faster algorithm is now used to find a vertex in Max Intensity mode;
• PointSize equal to zero now makes point ROIs invisible;
• redesigned UI a bit, optimized shader changes;
• new additional options for silhouette surface rendering mode (transparent and front culling);
• added option to clip ROIs, not only volume;
• changed "Crop" name to "Clipping" everywhere (incl bvv-playground), as a more precise term.

0.3.6

• ROI's surface rendering is performed using mesh now, so a variety of lighting became available: plain, diffuse, shiny, silhouette;
• Cross-section (plane) ROI render a bit tweaked to fit these new renders;
• changed the alignment of elements in different settings dialogs;
• moved tracing settings from the RoiManager settings dialog to separate dialogs for semi-auto and one-click. They are invoked by double-clicking corresponding icons now;
• updated to bigdataviewer-image-loaders v.0.6.4, thanks to @NicoKiaru a lot of unnecessary IO code is removed (loading 8-bit images to BVV as 16-bit).

0.3.5

• added check for self-intersection during "one-click" tracing to avoid infinite circular tracing;
• adjusted initial canvas render settings a bit;
• added ROI and intensity interpolation settings to Straighten and Crop extraction dialogs.

0.3.4

• added lazy loading of BioFormats using bigdataviewer-image-loaders;
• switched to bvv-playground v.0.1.2 that allows to apply transform to 'crop' function;
• added 'on-the-fly' data deskew of Zeiss LLS7 CZI files;
• as a plug, wrote modified methods from bigdataviewer-image-loaders (in a pretty ugly way) to load 8-bit data as 16-bit, since BVV supports only 16-bit texture;
• added possibility to Streighten all visible curve ROIs and save results as TIF files;
• added possibility to show CropBox and extract cropped volume;
• double-click on the ROI list makes the viewer focus on the clicked ROI volume;
• added time point to the measurements Results table;
• the last added vertex for all ROIs (except Point3D) is now displayed with a square around the point;
• some interface adjustments, mostly auto-expanded ROI list.

0.3.3

• switched to bvv-playground v.0.1.1, updated to bvv v.0.3.3;
• minor code refactoring;
• for timelapse datasets "current point" now shows ROI only at the current timepoint.

0.3.2

• added "one-click tracing", so far initial, "proof-of-concept" version;
• In "semi-auto" trace mode initial user click of the user (around intensity maximum) is further refined by finding the local maximum in the saliency (TraceBox) space;
• Fixed a bug of "on-screen" ROI selection in case some of the curves have only one vertex;
• Deleting a segment of LineTrace3D ROI is now possible without entering TraceBox mode;

0.3.1

Bug fix: conversion from float to unsignedbyte for "trace vectors" changed for the new version of imglib2 (now 6.1.0).

0.3.0

Major update: time addition

• added the possibility of loading imaging data containing a time dimension;
• each ROI is now assigned to a specific time point/frame. It can be changed in the ROI settings;
• ROI save csv format slightly changed;
• ROIs are now measured at specific time points;
• straighten curve command works on timelapse data;
• split volume across the plane ROI command works on timelapse data;
• added import of Point3D ROIs from Trackmate XML files;
• added possibility to see ROIs from previous or future time frames with adjusted transparency;

Other changes:

• for Point3D ROI added the possibility to render it as a circle (in outline/wire modes), not as a disk;

0.2.1

• fixed a bug when the very last segment of curve-like ROI was not removed from the scene;
• finally fixed Point3D shader for the proper scale and window aspect ratio;
• added intensity/SD measurements for Point3D ROI (sphere of 0.5*floor(Point size) radius);

0.2.0

Major update concerning curves' shape interpolation and measurements:

• line profile and intensity measurements now take into account "curve thickness" parameter;
• new shortcut "select ROI by clicking on the volume" with E;
• added Spline interpolation option and resampling along the arclength;
• added a "straighten curve" option to extract the volume along a curve (using RMF);
• rewrote generation of contours built around curves using "rotation minimizing frame" (RMF). Implemented two methods for that Wang et al 2008 and experimental;
• Line profile intensity/coalignment measurements are now done based on resampling the original curve with a step of the smallest voxel dimension (depending on shape interpolation);
• now line resampling in voxel/smooth modes happens based on "honest" linear interpolation;
• displayed curve-like ROIs' thickness is now independent of voxel anisotropy. It is measured in smallest voxel size units;

Other changes:

• ROI and line profile measurements are running in a separate thread now;
• joined many common PolyLine3D and LineTrace3D functions to AbstractCurve3D class;
• renamed Subvoxel mode to Smooth;
• for linear intensity interpolation now ClampingNLinearInterpolatorFactory is used;
• option to specify the distance between curve's pipe contours in wireframe render mode;
• added automatic dataset centering in the 3D view window upon voxel size change;
• added more digits to the voxel size panel;
• separated construction of cylindrical pipe's contours around polyline to geometry.Pipe3D class;
• refactored VisPolyLineScaled module, hopefully, now it is easier to read and it is better organized;
• VisPolyLineScaled now requires tangents at point locations;
• immediate update of ROIs render on interpolation settings change;
• changed icons for Line Profile and measurements export;
• changed visualization of LineTrace3D to one continuous segment.

0.1.4

• added a possibility to export "Line profile" and "Coalignment" measurements of all ROIs to a csv file;
• added "Coalignment" measurement, i.e. angle between a specified direction vector and all filament's points;
• added the name of the ROI Group to the measurements table;
• added adjustable parameters for the BVV rendering in the start menu and "View/Crop" options;
• adjusted Brightness/alpha settings of TraceBox are preserved during tracing;
• the same brightness/alpha preservation also works now for the tracing channel;
• added animation transition time as a configurable parameter.

0.1.3

bug fix

• floating point decimator in the voxel size is now permanently dot and does not depend on the system settings.

0.1.2

bug fixes

• initial scaling transform of the volume is fixed;
• brightness dialog spinners range is checked;

0.1.1

• fixed initial values of "brightness" sliders to be equal to internally specified by the plugin;

0.1.0

Major update. Moved to a modified version of BVV, which allowed:

• much faster crop without lag (now in shaders);
• new "brightness and color" dialog;
• possibility to switch from "max intensity" to "volumetric" rendering (shortcut P);
• first extra "dummy" channel is now removed (so hopefully, less confusion);

Other changes:

• works with BigDataViewer XML/HDF5 files;
• changed initial volume orientation (transform) at the start;
• made a separate "Settings" button for the navigation panel;
• some new parameters there: animation speed, mouse snap area;
• added "Zoom and crop" option;
• added "remove crop" shortcut X;
• added shortcut 3 for XZ view;
• XY, YZ, XZ views/shortcuts now work on cropped and TraceBox views;
• shrank and moved up "Voxel size" panel;
• added Cross-Section ROI (or Plane) and possibility use it to slice volume in two;
• added AbstractRoi3D class and moved many common methods there;
• fixed decimal separator issue with opacity value in the settings;

0.0.5

Major update

• "Measure" tab is added, including curve characteristics measurement settings and "Plot Profile" button;
• added a general smoothing parameter for displaying and measuring shapes (size of moving average window);
• added 16- and 32-bit TIF images support. For now, 32-bit just gets rescaled using min and max to 16-bit, so measurements give these rescaled results;
• in "trace mode" added V shortcut that starts a new trace;
• added voxel dimension to ROIs file, plus it scales the dataset accordingly when ROI file is loaded (thanks to Oane Gros feedback);
• exception caused by the addition of the point with the exact coordinates in Polyline mode is fixed (thanks to Oane Gros feedback);
• orientation of vectors is included in semi-auto tracing;
• fixed Groups loading list update;
• refactor ROI loading, some bug fixes;

0.0.4

large update, alpha release;

• added Groups for ROIS;
• help tab;
• specifications for the voxel size/tracing parameters in 3D;
• option to trace curve outside of crop area;

0.0.3

• added multicolor image support (still they should be 8-bit);
• added zoom-in by click option (shortcut D) / and zoom-in box size adjustment in options;
• added reading image range from ImageJ tiff and setting it to display;
• adjusted display range for each source/channel to [0..255];

0.0.2

• first version released for internal testing;
• works with one color 8-bit images only;