source: trunk/loci/visbio/whatsnew.txt @ 1745

Revision 1745, 19.3 KB checked in by curtis, 13 years ago (diff)

Update what's new to v3.31a.

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
[1745]1v3.31a - Friday, November 3, 2006
3- TWEAK: Ability to change Look & Feel on the fly
[1725]5- FIXED: Exception when exporting datasets
[1492]6- FIXED: Layout bugs with some Look & Feels
[1238]9v3.30 - Thursday, August 10, 2006
[1238]11- ADDED: File formats support is now in standalone Bio-Formats package
[1009]12- ADDED: Native DICOM support (eliminates dependency on ImageJ)
13- ADDED: Support for Olympus FluoView FV1000 (OIF & OIB) formats
14- ADDED: Support for Andor Bio-Imaging Division TIFF format
[1021]15- ADDED: Support for Encapsulated PostScript (EPS) format
[1009]16- ADDED: Support for Amersham Biosciences GEL format
17- ADDED: Support for Leica Image File Format (LIF)
18- ADDED: Support for Nikon Electronic Format (NEF)
19- ADDED: Support for Imaris (IMS) format
20- ADDED: Support for Openlab RAW format
21- ADDED: Support for OME-XML format
22- ADDED: Option to use 3D texturing in volume rendering
23- ADDED: Option to use nicer transparency blending
[1017]25- TWEAK: Better initial guess for dataset name
[1021]27- FIXED: Reversed Y-orientation in arbitrary slices
[1009]28- FIXED: Eliminated dependency on QuickTime for MOV, PICT and Openlab LIFF
29- FIXED: Eliminated dependency on Jakarta POI for Image-Pro IPW and Zeiss ZVI
[1016]30- FIXED: Avoid horizontal scroll bar in task list for long status messages
[1238]31- FIXED: Eliminate Java 1.5 XML parser warnings
[1009]32- FIXED: Bug in text overlays
[1021]33- FIXED: Other minor bugfixes
[627]36v3.22 - Tuesday, January 24, 2006
[590]38- ADDED: Interface for computing transform results with external system calls
[627]39- ADDED: Ability to switch between OpenGL and Direct3D modes on Windows
[627]41- FIXED: A few minor bugfixes
[590]44v3.21 - Monday, December 12, 2005
[587]46- ADDED: Support for Image Cytometry Standard (ICS) format
[586]48- FIXED: LZW compression now uses horizontal differencing
[579]51v3.20 - Tuesday, November 29, 2005
[579]53- ADDED: Rewrote TIFF export to save incrementally (uses much less memory)
54- ADDED: Option to use LZW compression when exporting TIFF files
[575]55- ADDED: Support for Image-Pro Sequence (SEQ) format
[579]56- ADDED: Support for Image-Pro Workspace (IPW) format
[582]58- TWEAK: Smaller download size
[577]60- FIXED: Grayed out thumbnail generation stop button
[572]63v3.19 - Wednesday, November 9, 2005
65- ADDED: Support for Gatan Digital Micrograph DM3 format
67- FIXED: Serious bug with single images
[567]70v3.18 - Friday, November 4, 2005
72- ADDED: Support for PerkinElmer file format
74- TWEAK: Additional menu shortcuts
[563]76- FIXED: Rewrote arbitrary slicing logic to be more efficient
[567]77- FIXED: Z axis bug with multiple data objects in a single 3D window
78- FIXED: Scaling bug with arbitrary slicing of some data
79- FIXED: Data object reordering in 3D displays (Up/Down buttons)
[570]80- FIXED: Dataset importer buttons staying greyed out after an error occurs
[556]83v3.17 - Friday, October 28, 2005
[548]85- ADDED: Support for Deltavision file format
[555]86- ADDED: Support for Leica file format
87- ADDED: Zeiss ZVI reader metadata parsing
88- ADDED: Partial support for multiple dimensional axes per file
[547]89- ADDED: Ability to view OME-XML/OME-TIFF metadata in dataset metadata viewer
[555]91- TWEAK: Smarter autodetection of dimensional axis types
[542]94v3.16 - Monday, October 17, 2005
96- TWEAK: Differentiate between QuickTime for Java missing versus expired
98- FIXED: Report thumbnail recomputation properly when data objects are altered
[537]101v3.15 - Friday, October 14, 2005
[531]103- ADDED: Separate task tracking for each background task VisBio is performing
104- ADDED: Rearrange main VisBio window to be more streamlined
[542]106- TWEAK: Added plugins folder for use with ImageJ from within VisBio
[529]107- TWEAK: Report more information during initial dataset creation
[530]108- TWEAK: Don't create errors.log unless necessary
[531]109- TWEAK: Eliminate some debugging messages from the output console
[537]110- TWEAK: Better error messages when QuickTime is not installed
[536]112- FIXED: Bug in non-image data objects (arbitrary slices, overlays)
113- FIXED: Ignore thumbnails in Zeiss LSM images
114- FIXED: Better detection of QuickTime v7.0 for Windows
[537]115- FIXED: Ignore first image of an Openlab file only if it is "Original Image"
[526]118v3.11 - Monday, October 10, 2005
120- FIXED: Bug in Zeiss LSM reader
121- FIXED: Bug in Metamorph STK reader with multi-image files
122- FIXED: Ugly status messages with volume rendering and ImageRendererJ3D
[521]125v3.10 - Monday, October 3, 2005
127- ADDED: Support for IPLab file format
[523]128- ADDED: Better support for Zeiss LSM, Metamorph STK and Fluoview TIFF
130- TWEAK: Quicker initial processing of multi-file datasets
131- TWEAK: More efficient image display in many cases (using ImageRendererJ3D)
133- FIXED: Disallow "In 3D" display option when Java3D is not installed
[508]136v3.09 - Monday, July 25, 2005
[508]138- ADDED: Ability to export data objects directly to ImageJ
[503]139- ADDED: Folder chooser to export dialog for specifying which folder to use
[509]141- TWEAK: Warn user if export to 24-bit RGB will truncate data values
[501]143- FIXED: Ignore first image (pure white RGB) of Openlab datasets
[495]146v3.08 - Tuesday, July 19, 2005
148- ADDED: Ability to specify pixel type for datasets uploaded to OME
149- ADDED: A command-line tool for uploading datasets to OME: "omeul"
[515]151- FIXED: More robust visbio.tmp deletion on program exit
[494]154v3.07 - Friday, July 15, 2005
[494]156- ADDED: Ability to export 8-bit grayscale, 16-bit grayscale, and 32-bit
157         floating point TIFFs (in addition to 24-bit color TIFFs); which format
158         to use is auto-detected
[493]159- ADDED: Option to configure eye separation distance
161- FIXED: Problem with eye separation in stereo mode
[492]164v3.06 - Tuesday, July 12, 2005
[491]166- FIXED: Bug in MATLAB transform for data with only one range component
167- FIXED: Bug in collapse and projection transforms where some axes don't work
[492]168- FIXED: Problem uploading datasets to an OME database; due to updated XML-RPC
169         processing logic on the OME backend, please use the latest version of
170         OME from CVS for now if you want to take advantage of VisBio's OME
171         upload capabilities
174v3.05 - Friday, July 8, 2005
[459]176- ADDED: Copy, paste and mass distribution overlay functions
[480]177- ADDED: Initial implementation of MATLAB-VisBio interface
179- FIXED: Remove selected overlays only affects the current dimensional position
[485]180- FIXED: Improper color summing when Java3D not present
[488]181- FIXED: Problem adjusting maximum heap on Mac OS X
[465]182- FIXED: Add loci-ome-xml.jar to launch scripts
[458]185v3.00 final - Wednesday, June 8, 2005
187- ADDED: "Sample datasets" menu for automatically downloading sample data
[437]188- ADDED: Ability to specify dataset's physical dimensions in microns
[418]189- ADDED: More robust XML-based program states
[406]190- ADDED: Options for controlling thumbnailing parameters
191- ADDED: Options for controlling image stack parameters
[378]193- TWEAK: Option to toggle hiding of all windows when main window is minimized
[364]195- FIXED: Subsampling image scaling bugs (relating to improper domain sets)
[360]196- FIXED: Bug in image sequence capture when no file extension is given
[412]197- FIXED: Disallow invalid combinations of stack settings
[450]198- FIXED: Better subsampling error checking
[352]201v3.00 beta5 - Tuesday, April 26, 2005
203- ADDED: Data export: save a data object to a file series on disk
[256]204- ADDED: Ability to download images from an OME database (OME image transform)
[321]205- ADDED: Dragging selected overlays with the pointer tool moves them
[270]206- ADDED: Support for key/value pair command-line parameters
[355]207- ADDED: Ability to launch VisBio through a web browser with Java Web Start
[296]208- ADDED: Support for PNG images
[312]209- ADDED: All online help topics are written
[270]211- TWEAK: VisBio icon is now used instead of default Java cup icon
[292]212- TWEAK: System property for controlling native frame decoration (for L&Fs)
[332]213- TWEAK: Only one VisBio instance allowed to run at a time
214- TWEAK: Secondary instances pass parameters to active instance before quitting
[352]215- TWEAK: Remove OME-CA XML state logic completely
[317]217- FIXED: Several overlay bugs eliminated
[292]218- FIXED: More robust behavior when Java3D is not installed
[296]219- FIXED: More descriptive error messages if VisBio fails to start up
[249]220- FIXED: Combo box width for Windows Look & Feel
[241]221- FIXED: Lots of little bugfixes
[229]224v3.00 beta4 - Wednesday, March 16, 2005
226- ADDED: Volume rendering
[196]227- ADDED: Arbitrary slice data transform
[221]228- ADDED: Data cache system for managing full-resolution data in memory
229- ADDED: Expanded VisBio help system
[196]230- ADDED: Pressing arrow keys on a display cycles through dimensional positions
231- ADDED: Ctrl + arrow keys on a display causes it to pan
232- ADDED: Shift + up/down arrow keys on a display zooms in and out
233- ADDED: Shift + left/right arrow keys on a display rotates around Z axis
234- ADDED: Shift + ctrl + arrow keys on a 3D display rotates around X and Y axes
235- ADDED: Typing characters on a display affects selected text overlays
236- ADDED: Pressing delete on a display removes selected overlays
[221]238- FIXED: Rewrote TIFF importer to be an order of magnitude more efficient
[181]239- FIXED: Broken data transforms (sampling, max intensity, collapse, spectral)
[196]240- FIXED: Upside down ZVI datasets
[181]241- FIXED: Several overlay data transform bugs
242- FIXED: Several window centering issues
[162]245v3.00 beta3 - Wednesday, February 2, 2005
[119]247- ADDED: Overlays data transform for creating overlay annotations
248- ADDED: "Immediate" data transforms that ignore full-resolution burn-in delay
[95]249- ADDED: Individual control over each data object's color settings
250- ADDED: Transparency settings within data object color settings
251- ADDED: Proper management of multiple data object Z-ordering
[152]252- ADDED: Preload most classes to speed up VisBio response time
[76]253- ADDED: Controls for altering how long full-resolution burn-in is delayed
[119]254- ADDED: Ability to toggle whether consoles pop up when output is produced
[71]255- ADDED: System button for dumping system properties to output console
257- TWEAK: Dataset chooser displays progress bar while analyzing file pattern
258- TWEAK: Dataset chooser jumps to directory specified in file pattern field
[136]260- FIXED: Occasional multiple data transform burn-in deadlock
[162]261- FIXED: A bunch more little bugfixes
[62]264v3.00 beta2 - Wednesday, October 27, 2004
[56]266- ADDED: Preliminary support for Zeiss LSM and ZVI file formats
267- ADDED: Continue work on comprehensive state support in XML format
[50]269- FIXED: Mac OS X menu bar behaves much better
[56]270- FIXED: Various other bugfixes and improvements
[32]273v3.00 beta1 - Wednesday, September 1, 2004
[21]275- ADDED: Support for Metamorph STK file format
[28]276- ADDED: Support for Olympus Fluoview file format
[24]277- ADDED: Support for Openlab LIFF file format (requires QuickTime for Java)
[2]278- ADDED: Dimensional collapse transform
279- ADDED: Weighted multispectral component mapping transform
[21]280- ADDED: Ability to change maximum memory value from the System panel
281- ADDED: Ability to change graphical "Look & Feel" from the System panel
282- ADDED: Begin work on comprehensive save/restore/undo/redo using OME-CA XML
284- FIXED: Tons of bugfixes and improvements
[21]286- TWEAK: Switched Windows distribution to ZIP file; no need for an installer
[28]287- TWEAK: Windows distribution now defaults to "JGoodies Windows" Look & Feel
288- TWEAK: Linux distribution now defaults to "JGoodies Plastic 3D" Look & Feel
[21]289- TWEAK: Fixed up all distribution packages
292v2.31 - Thursday, July 1, 2004
294- ADDED: "Burn" button to force full-resolution burn-in
295- ADDED: Automation option to delay burn-in until "Burn" button is pressed
296- ADDED: Measurement flags (markers without a fixed dimensional position)
298- FIXED: Long delay before first screen dataset is computed
300- TWEAK: Switched Windows installer to JSmooth + Inno Setup
301- TWEAK: Switched Linux distribution to a simple script file
303- GONE: Eliminated Solaris distribution
306v2.30d - Monday, June 14, 2004
308- FIXED: Bugs when Java3D is not installed
309- FIXED: Greatly improved burn-in function / slider responsiveness
312v2.30c - Tuesday, April 13, 2004
314- FIXED: Issue with "Open file" functionality
315- FIXED: Bug when nothing is mapped to Z-axis
318v2.30b - Tuesday, March 30, 2004
320- FIXED: Number doubling bug in file pattern detection logic
323v2.30a - Wednesday, February 18, 2004
325- FIXED: Minor data import bug
327- GONE: Old "import series" dialog box ("Import group" does everything)
330v2.30 - Monday, February 2, 2004
332- ADDED: Support for importing Olympus Fluoview TIFF format
333- ADDED: Improved file group pattern logic
334- ADDED: Yellow bounding box around current slice in 3-D display
335- ADDED: Parallel projection mode for 3-D display
337- FIXED: Full-resolution burn-in bug with arrow buttons
339- TWEAK: Raised volume rendering limit to 192x192x192 pixels
342v2.21 - Thursday, January 15, 2004
344- ADDED: Capture tab now uses AVI, to avoid Mac OS X QuickTime issues
345- ADDED: Drag and drop support (open files by dropping them onto VisBio)
346- ADDED: Full Windows installer now uses Java 1.4.x instead of 1.3.x
348- FIXED: Several serious export bugs fixed
349- FIXED: Full-resolution burn-in bugs finally tackled
350- FIXED: No more garbage when 3-D display is resized on Mac OS X
351- FIXED: Nasty dimensional slider upper bound + step size bug quashed
352- FIXED: Eliminated illegal fixed color range bounds bug
354- TWEAK: Better status bar messages
357v2.20 - Monday, January 5, 2004
359- ADDED: New animation code is choppier but saves tons of memory
360- ADDED: Status bar messages indicating current visualization status
361- ADDED: Option for automatically purging old screen datasets
363- GONE: Previous/next preview displays
366v2.10 - Monday, December 15, 2003
368- ADDED: Thumbnail disk cache (now data loads more than 20X faster!)
369- ADDED: Ability to view arbitrary slices superimposed in the 3-D display
372v2.04 - Friday, December 5, 2003
374- ADDED: Better movie capturing controls (e.g., adjustable frames per second)
375- ADDED: Better support for datasets with one image per file
376- ADDED: Better support for single images
377- ADDED: Better file group detection
378- ADDED: Menu shortcuts for common tasks
379- ADDED: Option for toggling status bar visibility
381- FIXED: Mac OS X Application menu items now work as expected
384v2.03a - Friday, November 21, 2003
386- FIXED: Deal with bugs preventing proper saving of QuickTime movies
388- TWEAK: Display positions on Capture tab list can now be given better names
391v2.03 - Wednesday, November 19, 2003
393- ADDED: Separate ij.jar, for upgrading ImageJ independently of VisBio
395- FIXED: Better QuickTime for Java detection on Windows XP
397- TWEAK: Better error messages when an error occurs during file import
400v2.02 - Monday, November 17, 2003
402- ADDED: Capture 3-D display sequences to QuickTime movie files
403- ADDED: Mac OS X version is now distributed as an application bundle
405- FIXED: Volume rendering toggle and resolution bugs fixed
406- FIXED: Direct color table alterations now work again, and are saved
407- FIXED: Potential Z-axis autoscaling issue fixed
408- FIXED: Bunches more save & restore bugs fixed (should be quite robust now)
409- FIXED: Some import/export bugs squashed
412v2.01 - Friday, September 5, 2003
414- ADDED: Undo is back, with multiple undo & redo support
416- FIXED: Many save & restore state bugs fixed
417- FIXED: Many measurement bugs fixed
418- FIXED: Various other bugfixes
421v2.00 - Friday, August 8, 2003
423- ADDED: VisBio now handles multidimensional image data with any number of
424         dimensions, not just 4-D across space and time
425- ADDED: Separate treatment of "raw" versus "screen" datasets, including
426         the ability to create multiple data samplings from the same source,
427         and detailed statistics regarding loaded datasets
428- ADDED: Flexible import/export logic handles multidimensional data distributed
429         across a group of files in any orientation
430- ADDED: QuickTime for Java now automatically detected, without the need to
431         muck around with
432- ADDED: Largely rewritten with a new code architecture offering greater and
433         more flexible extensibility of the system (write your own plugins!)
434- ADDED: Automatic "burn in" of full-resolution images while view is idle
435- ADDED: Separate "Edit Colors" dialog with lightning quick preview pane
436- ADDED: Multiple simultaneous arbitrary slices
437- ADDED: Intelligent automatic data sampling
438- ADDED: Warnings issued before performing memory-intensive operations
439- ADDED: Separate options screen with multiple categories of options
440- ADDED: VisBio startup screen displayed while VisBio loads
441- ADDED: More verbose display indicating what VisBio is doing while it's busy
442- ADDED: "Clean memory" button for forcing a Java garbage collection operation
443- ADDED: VisBio's built-in help updated to provide detail on new features
444- ADDED: Status bar
446- FIXED: Tons of bugfixes (and surely many new bugs--please report them!)
448- GONE:  Drift correction will be back with the next release
449- GONE:  Undo support will be back with the next release
[2]452v1.0 beta 3C - Wednesday, October 30, 2002
454- FIXED: NullPointerExceptions when running without Java3D (2-D only mode)
455- FIXED: Added "Snap now" button to measurement controls for immediately
456         snapping each measurement endpoint to its nearest slice
457- FIXED: Removed needless restriction on merging standard measurements
460v1.0 beta 3B - Friday, October 11, 2002
462- FIXED: Shift + left drag no longer selects measurements outside its bounds
463- FIXED: Non-selected lines can now be moved when there is a selection
464- FIXED: Eliminated bug where shift + left drag to highlight measurements
465         sometimes changed the color of the newly selected measurements
466- FIXED: Measurements are now added in a reasonable location when the 2-D
467         display is toggled off
470v1.0 beta 3A - Thursday, October 10, 2002
472- FIXED: Arbitrary slice & alignment triangle now always appear properly
473- FIXED: Arbitrary slice now updates correctly
474- FIXED: Alignment triangle no longer exhibits strange behavior after
475         restoring state
477- TWEAK: Improved thread usage relating to progress dialog
480v1.0 beta 3 - Friday, October 4, 2002
482- ADDED: Drift correction--a tool for alignment of image stacks
483- ADDED: Now two kinds of standard--"2-D standard" distributes measurement
484         across all slices of all timesteps, whereas "3-D standard" distributes
485         measurement across all timesteps with the current slice values
486- ADDED: More intuitive mouse controls--now left button manipulates
487         measurements, arbitrary slice and alignment triangle, while right
488         button manipulates the display view (rotate, pan and zoom)
489- ADDED: Snapshots of the currently displayed image can now be sent to ImageJ
490         to be manipulated ("File/Send snapshot to ImageJ" option)
491- ADDED: Memory usage information is now displayed in the main window
492- ADDED: Option to disable behavior where measurement endpoints snap to the
493         nearest slice
494- ADDED: Option to have each group of controls displayed in a separate,
495         floating window rather than as a series of tabs
496- ADDED: Color range can now be set separately for each color component
497- ADDED: Old console window eliminated in favor of graphical console window
498         system
499- ADDED: Completed initial version of VisBio's online help
501- FIXED: Fixed bug where certain multipage TIFF files were loading incorrectly
502- FIXED: Custom color tables now saved properly to state file
503- FIXED: Import dialog's series detector now works with file series that have
504         leading zeroes (e.g., "AREA0007")
505- FIXED: Import dialog's series detector now works with files that have very
506         long numbering schemes (e.g., "")
507- FIXED: Disallow 2-D standard measurement lines spanning multiple slices
508- FIXED: Rightmost value of color widgets can be properly manipulated now
510- TWEAK: Quit operation can now be canceled
513v1.0 beta 2A - Tuesday, August 27, 2002
515- FIXED: A single file containing an image stack is now handled properly as a
516         time series if "treat each file as a slice" is selected.
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