VAST Lite Version 1.4.1 (c) June 2nd, 2022 by Daniel Berger, Lichtman Lab, Harvard VAST is a Volume Annotation and Segmentation Tool for microscopic image stacks. It runs on PCs with 64-bit Windows 7 or later. This version of VAST is free of charge and may be distributed freely, but not sold. Commercial usage is allowed. You are using this software at your own risk. Version 1.4.1 implements the following improvements over version 1.4.0: MAJOR NEW FUNCTIONS -------------------- - New 'Tool Layers' support 'Chunked Region Collector' for agglomeration of automatic segmentations with skeletons - Support for loading datasets from many new online sources via .vsvi files: Multitile images (graylevel and RGB) and Neuroglancer formats, including 'compressed_segmentation' data and Google's 'Precomputed Sharded' format with and without OAuth2 validation, supporting data stored in Google Cloud Storage and Amazon Web Services OTHER NEW AND IMPROVED FUNCTIONS --------------------------------- - Accessibility: Keyboard navigation in tool window lists and trees can now be reenabled in Preferences - Accessibility: F2 now triggers label editing in Segmentation Colors and Annotation Objects trees - Accessibility: Cleaned up TAB behavior in Coordinates, Drawing Properties, and Filling Properties tool windows - Added 'Generate Skeletons From Other Layers' to Annotation Objects menu - Added 'Arrange / Collect by Name Into Selected Folder' to 'Annotation Objects' menu - Added control button functions "Append Text to Label", "Replace Label Text" and "Replace Part of Label Text" for annotation objects and nodes - Added bulk agglomeration inclusion and exclusion functions to node context menu - Added optional local file cache functionality for VSVR layers - Added 'Randomize all colors of subtree' to annotation objects context menu - Blend mode 'Black transparent' can now be set for EM layers - Node context menu now has functions to search for node labels (full and partial) - 'Show node information' in node context menu now includes DFS number, Xflags and EXT value - Node context menu now has a function to search for nodes with specific EXT value - Annotation objects: Subtrees can now be colored with a selected color range - Segment Colors and Annotation Objects menu: 'Arrange / Move to Parent Level' added - Annotation Objects menu now has a function 'Copy selected EXT list to clipboard' - Annotation layer skeletons now obey Alpha/Selalpha for subtrees in 2D view - 'Arrange / Sort Siblings by ID' added to Annotation Objects context menu - Added 'Z-Jump Up' and 'Z-Jump Down' to Control Button functions - Control buttons now allow to show/hide specific layers - Skeletons can now be copied from one annotation layer to another (single, folder, all) - Annotation Objects Menu / 'Save Skeleton Data ...' now also saves EXT and XFlags fields of nodes - Extended .vsvi format to allow for custom mip folder names - Extended .vsvi format to allow for custom image block sizes per mip level - Extended .vsvi format to allow for image block names using pixels instead of block counting, including +1 upper limit - When in annotation mode and after a node search for nodes with certain labels or EXT was used, F3 pressed in the 2D window or the schematic viewer now triggers 'search again' - Added 'Delete parent edge (split tree)' to node context menu - Implemented multi-threaded loading of image stacks from .VSVI (define number of threads in VSVI file using "NumberOfImageLoaders") - Color channel remapping now also works for color-mapped 64-bit image layers - Added 'white' as standard target color for color channel remapping - Added lengths per edge type to Annotation Objects menu / Annotation Object Information - Added 'Set parent edge type' to control buttons - Error messages for failing GPU initialization during startup added - Node catch distance for mouse cursor now follows 2D texture scaling - SHIFT NUM+ now goes to previous segment / previous annotation object. Also added to control buttons - Annotation layers now remember selected object and node and node label search string after saving - Sped up segmentation exporting to images by doing deferred upsampling only when necessary and changing the export order for multitile exports - Added display of nearby edges and nodes with dimming / scaling down. Parameters for this can be set in the Preferences - Added 'Toggle Exclude Node From Agglomeration' to control button functions BUG FIXES ---------- - Fixed image export range checking - Color picker now blocks GUI - Fixed a crash when 'Follow active node' was enabled in schematic viewer but the selected skeleton had no nodes - Removed recursive call in annotation list loading (caused stack overflow for large lists) - Fixed control buttons key trigger 9 and 0 - Fixed a bug in annotation list switching - Improved selecting different annoobject after annoobject deletion - Fixed a bug in file name handling when loading layers via the API - Fixed a crash after an annotation layer was saved for which the linked tool layer was removed - Expanded/collapsed colors of annotation objects are now set correctly when loading a vsanno file - Fixed a bug causing crashes when an annotation layer was removed and another one opened - Fixed volume export crop computation (Segment Colors menu / Export Volume Measurements) - Fixed pop-up behavior of some message windows - 2D view stretching of voxel data and paint cursor now changes immediately after the voxel size is changed ('Info / Volume Properties') - Cleaned up annotation layer 'Save' function (hopefully preventing crashes involving the schematic viewer) - Some fixes in the 'Segment Colors' / 'Export Volume Measurements' function - Fixed 'Arrange / Collect by name into folder', siblings and children for segments - Fixed a bug where vsanno files with skeletons with cases where both child nodes are at the same coords wouldn't load - Fixed a bug which prevented merging multiple .VSS/.VSSEG files at once (CAUTION: This function is still buggy!) - Fixed 'Set primary color of all immediate children' and 'Set secondary color of all immediate children' - CTRL and SHIFT key press is checked when switching to schematic viewer - Fixed a bug preventing loading 8-bit images from Google Cloud Buckets 3D VIEWER ---------- - 3D viewer: Standard render engine now respects independent X and Y voxel size - 3D viewer can now show skeletons in white API ---- - Fixed the function getchildtreeids in VASTControlClass.m - Fixed mip coordinate +Z boundary in API voxel export routines - API: Moving annotation objects now also works when the annotation objects toolwindow is not displayed - API: Added function settoolparameters(layernr, node, params) - Inherited color now included in the API function getannolayerobjectdata - Implemented API function 'setannoobject' for parameters label, nodecolor, edgecolor, userflags and userid - Fixed a crash when the API function setsegmentcolor() was called before the segment colors tool window was opened - API, VASTControlClass.m: 'flipflag' for getsegimageraw() should now work (needed reshape; kind of inefficient solution) - Added API function 'getscreenshotimageRLE' to API; getscreenshotimage has optional parameter switching to RLE transfer - Extended API function setannoobject with a few more parameters - API function addannoobject now also sets the color for skeletons - Added check in API functions addannoobject and setannoobject not to read over the end of provided arrays if they are too short - Increased the size of images that can be handled by the API function getscreenshotimage() VASTTOOLS ---------- - VastTools: Added overlap measurement export between two segmentation layers - VastTools: Added 'Isosurfaces from screenshots, one object per color' to mesh exporter - VastTools: Fixed projection image exporting for cropped regions - VastTools: Added Z Span parameter to reduce memory footprint when computing projection images - VastTools: Added 'Disable network warnings' to vasttools 3d model exporting - VastTools: 3D model exporting uses 'getscreenshotRLE' if surfaces are exported from screenshots - VastTools: 'Export Particle Clouds' can now generate particles from skeleton nodes - VastTools: 'Export Particle Clouds' can now save all exported models to a single obj file - VastTools can now export colored Neuroglancer links for the Human H01 C3 segmentation, as agglomerated with skeletons / tool layers