Changes with NeuronStudio 0.9.92 *) If the slice viewer is active, manually placed nodes will acquire the Z coordinate of the slice view if in XY view mode in the 2D window. *) The maximum DTS for manual spines now is calculated by bubbling up from the user defined center point, but only using the attachment edge as a reference. *) Spine attachments for manual spines can be made more user defined by clicking and dragging while using the spine tool. *) Hollow 3D shapes (e.g. spines and vertices) are now drawn as actual circles that stay aligned with the camera position (billboarding). *) Implement new clump building algorithm for better discretization of merged spines and complex spine shapes. Changes with NeuronStudio 0.9.90 *) Implement angle-based algorithm for removing spurious voxels on the last layer of the spines. *) Retain spine voxels after analysis for visualization. Global .ns setting can override this (saves memory). *) Remove non-spine voxels after analysis to reduce memory consumption. *) Create new spine voxel visualization mode in both 2D and 3D. *) Compute true spine axis using a distance to surface and distance to branch "map". *) Use residual smear value in the calculation of a spine's distance to branch map. *) Make main menu item View >> Spine Axes show this new true axis in both 2D and 3D, instead of the approximate axis as before. *) .ns file is now called config to avoid problems with the leading period in Windows systems. Similarly .log and .settings are now just called log and settings respectively. Changes with NeuronStudio 0.9.88 *) Initialize settings as the user defaults over the program defaults if they exist. *) Settings should be written to file when the user applies new neurite filtering settings, or cancels after applying new ones. *) Implement algorithm for repositioning junction vertices according to directions of incoming branches. *) Create setting for repositioning junction vertices and add to neurite settings. . *) Removed "exclude neurite voxels" from threshold settings for spine analysis. *) Implement new, more efficient and robust pruning algorithm *) Put the discretization ratio back into the interface and save it along with the other settings. *) Add items to the 3D window menu for selecting the mouse mode (tool). *) Render splats as points when adjusting ROI, if point pre-rendering is enabled. *) Fix 32-bit integer overflow of file size bug when opening a RAW image. *) Fix bug in 3D selection of objects caused by integer overflow. *) Allow ROI manipulation in the 3D window. *) Generate 2D and 3D rayburst sampling cores dynamically at startup, rather than reading from files. *) Incorporate TSS code into the program as an image filter. Provide a dialog box for setting parameters. *) Implement dialog box for setting parameters for the brightness/contrast image filter *) Implement dialog box for setting parameters for the dynamic range image filter. *) Make resize filter behave like the subsample filter in terms of resetting the slice index, regions of interest, etc. after processing. *) Fix bug in reading of neck diameter for spines file. *) Computer head and neck center of mass. Allow reading and writing of these to a spine file. *) Add number of branch points per sholl sphere to the sholl analysis. *) Preserve seed location if "Load Initial" button is pressed in the defaults tab of the settings dialog box. *) Change voxel size tab in the settings dialog box to a volume tab. *) Add labeling type to the volume tab of the settings dialog box. This setting is read and write to the settings file as well. *) Add residual smear type to the volume tab of the settings dialog box. This setting is read and write to the settings file also. *) Use volume labeling and residual smear type to implement algorithmic changes to allow tracing to work better, especially in membrane labeled data. *) During voxel scooping (i.e. tracing), use two running thresholds for membrane labeled volumes, one for constructing the axis, and one for the rayburst. Changes with NeuronStudio 0.9.86 *) Compute thresholds for the edges of the model and use in spine detection. *) Make 3D window retain state for rendering options even after the 3D window is closed. *) Render splats as points when rotating, translating, window resizing, grafting, and detecting spines. Add menu option to enable or disable this feature. *) Dont allow the user to enter 0 for any of the voxel sizes. Currently the program will replace a zero with 0.1. *) If the volume is 2D, then no matter what the user enters for the Z voxel size always replace it with 1.0. *) Update all filters including the multi-threaded ones to only operate on the current visualized region of interest. *) Enable saving the image stacks in a different pixel format for both RAW and TIFF images *) Have "all supported formats" for Open dialog box for image stacks, and select it by default. *) Enable setting the seed in the 3D window. *) Enable adding spines, neurites, and samples in 3D. *) Allow selection of neurites, spines, and samples in 3D using a drag rectangle, and single click. *) Check for overwrite of current files in saving volume and projections. *) Dont deselect the two selected nodes after user manually adds or removes and edge between them. *) When adding a node, or a series of nodes using the semi-auto tool, they should all become selected, all others delesected. *) If exactly one node selected when adding a node or a series of nodes, connect the new nodes to that one automatically. *) Make grid step size update whenever the settings are changed. Changes with NeuronStudio 0.9.80 *) Implement new spine declumping algorithm which clumps voxels based on intensity. Use clumps as a map during the building phase. *) Implement Sholl Analysis of dendrites and spines. *) Fix bug that causes 12-bit data not to be written when saving image. *) Allow sub-voxel translation and rotation. *) Allow reading of Zeiss LSM image files. Voxel size is automatically set if present in the file. *) Add "Transpose Children" feature to allow users to manually control the section labeling algorithms. *) Add checkbox to the neurites tab of the settings window to allow the user to turn on or off scattered sampling during tracing. *) Create a "flip optical axis" image filter which reverses the data along the Z (optical) axis. *) Create red, green, blue, and yellow palettes for the 2D display. *) Allow visualization of section ID's in the 2D display. *) Allow visualization of the sholl spheres (circles) in the 2D display. *) Fix bug in intensity mask palette for slice view. Only true zero and true max intensity for 12 and 16 bit images are mapped to blue and red respectively. *) Allow saving the spines file in comma separated format (CSV). *) Create new magnet tool. Can click and drag on vertices for easy manual editing. *) Create gamma correction palettes for a gamma value of 1.7 and 2.2. *) Allow visualization of the spine ID's in the 2D display. *) Allow visualization of a 3D grid behind in the dataset in the 3D display. *) Allow the user to manually adjust the spine ID's using keyboard commands. *) Allow selection and deselection or vertices, spines, and measurements in 3D by double clicking. *) Fix bug in the fixed threshold value for neurite tracing. Value must range from 0 to 255 and be rescaled for 12 and 16 bit data. *) Clip the size of the main window when launching the program to the boundaries of the screen. Reposition if necessary as well. Changes with NeuronStudio 0.9.64 *) Correct bug in fixed threshold tracing. *) Allow changing diameter of selected spines. *) Allow changing diameter of last/current sample. Changes with NeuronStudio 0.9.62 *) Create recompute spine attachment function and menu command. *) Handle spaces in spine class names properly (replace with dashes). *) Fix bug in reading and writing of long spine class names. *) Add an example classifier to distribution. *) Prevent spines with no type (invalid) from being added to the current classifier. Changes with NeuronStudio 0.9.60 *) Compile FANN into NeuronStudio. *) Create interface for creating a new classifier. *) Create capability to load and save a classifier. Loading makes classifier active. *) Enable ability to see which classifier is active. *) Ability to add selected spines as training data to active classifier. *) If no active classifier use default decision tree-based one. *) Create interface to edit classifier training data. *) Allow changing diameter of manually added spines. *) Update spine loading and saving to allow user defined types. *) Output new field in spine output with distance to soma. *) Prevent spheres in node from overtaking frusta in DTS computation. Changes with NeuronStudio 0.9.50 *) Fix bug in HOC file format output when multiple somas are present. *) Implement slice viewer widget. *) Make automatic tracing procedure more responsive to cancellation. *) Use random sampling during the tracing procedure for increased performance. *) Make slice viewer control the Z coordinate of the seed if set in Forward (XY) view. *) Calculate the total dendritic length of the model and display in the Model Info dialog box. *) Disallow adding measurements or manual spines if the user clicks outside the boundaries of the region of interest (ROI). *) Limit the progression of the semi-manual tracing to the boundaries of the ROI. *) Make sure the seed location and slice viewer's current slice are limited to the boundaries of the ROI as well. Changes with NeuronStudio 0.9.48 *) Fix slice viewer rendering bug. Changes with NeuronStudio 0.9.46 *) Allow slice viewer to control Z-position of manually added spines and measurements. *) Create interface for controlling the global threshold applied to the volume rendering. *) Fix bug in reading true 16-bit TIFF images. *) Fix bug in Rayburst code where rays travel outside the image. *) Allow skipping the generation of the volume rendering if View >> Image not checked in the main menu. *) Allow zooming to 256 times the size of one pixel. *) Enhance rendering speed of 2D projections, especially for large datasets. Changes with NeuronStudio 0.9.44 *) Display edge order numbers in the 2D window. *) Remove expiration date (perpetual license). *) Fix display bug where 'Fit Image' and/or 'Actual Pixels' selected without 'Center & Limit Image' being active. *) Fix crash when resize filter selected. Set region of interest (ROI) to 100% of the new size. *) Move gamma correction to the palette sub-menu. Gamma correction factor of 1.7 and 2.2 available. Also visible in slice view mode. *) Display spines as ellipses with diameter equal to the head size. *) Enhance file name sequence detection. Support for arbitrary placement of series numeral. Changes with NeuronStudio 0.9.42 *) Render vertices by order and section. The parent edge is used to determine the values. *) Flash hidden vertices and spines. F3 shortcut key added. *) Output attachment x,y,z coordinate to spine file. Columns are named ATTACH-X, ATTACH-Y, and ATTACH-Z.