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
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1v3.31a - Friday, November 3, 2006
2
3- TWEAK: Ability to change Look & Feel on the fly
4
5- FIXED: Exception when exporting datasets
6- FIXED: Layout bugs with some Look & Feels
7
8
9v3.30 - Thursday, August 10, 2006
10
11- ADDED: File formats support is now in standalone Bio-Formats package
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
15- ADDED: Support for Encapsulated PostScript (EPS) format
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
24
25- TWEAK: Better initial guess for dataset name
26
27- FIXED: Reversed Y-orientation in arbitrary slices
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
30- FIXED: Avoid horizontal scroll bar in task list for long status messages
31- FIXED: Eliminate Java 1.5 XML parser warnings
32- FIXED: Bug in text overlays
33- FIXED: Other minor bugfixes
34
35
36v3.22 - Tuesday, January 24, 2006
37
38- ADDED: Interface for computing transform results with external system calls
39- ADDED: Ability to switch between OpenGL and Direct3D modes on Windows
40
41- FIXED: A few minor bugfixes
42
43
44v3.21 - Monday, December 12, 2005
45
46- ADDED: Support for Image Cytometry Standard (ICS) format
47
48- FIXED: LZW compression now uses horizontal differencing
49
50
51v3.20 - Tuesday, November 29, 2005
52
53- ADDED: Rewrote TIFF export to save incrementally (uses much less memory)
54- ADDED: Option to use LZW compression when exporting TIFF files
55- ADDED: Support for Image-Pro Sequence (SEQ) format
56- ADDED: Support for Image-Pro Workspace (IPW) format
57
58- TWEAK: Smaller download size
59
60- FIXED: Grayed out thumbnail generation stop button
61
62
63v3.19 - Wednesday, November 9, 2005
64
65- ADDED: Support for Gatan Digital Micrograph DM3 format
66
67- FIXED: Serious bug with single images
68
69
70v3.18 - Friday, November 4, 2005
71
72- ADDED: Support for PerkinElmer file format
73
74- TWEAK: Additional menu shortcuts
75
76- FIXED: Rewrote arbitrary slicing logic to be more efficient
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)
80- FIXED: Dataset importer buttons staying greyed out after an error occurs
81
82
83v3.17 - Friday, October 28, 2005
84
85- ADDED: Support for Deltavision file format
86- ADDED: Support for Leica file format
87- ADDED: Zeiss ZVI reader metadata parsing
88- ADDED: Partial support for multiple dimensional axes per file
89- ADDED: Ability to view OME-XML/OME-TIFF metadata in dataset metadata viewer
90
91- TWEAK: Smarter autodetection of dimensional axis types
92
93
94v3.16 - Monday, October 17, 2005
95
96- TWEAK: Differentiate between QuickTime for Java missing versus expired
97
98- FIXED: Report thumbnail recomputation properly when data objects are altered
99
100
101v3.15 - Friday, October 14, 2005
102
103- ADDED: Separate task tracking for each background task VisBio is performing
104- ADDED: Rearrange main VisBio window to be more streamlined
105
106- TWEAK: Added plugins folder for use with ImageJ from within VisBio
107- TWEAK: Report more information during initial dataset creation
108- TWEAK: Don't create errors.log unless necessary
109- TWEAK: Eliminate some debugging messages from the output console
110- TWEAK: Better error messages when QuickTime is not installed
111
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
115- FIXED: Ignore first image of an Openlab file only if it is "Original Image"
116
117
118v3.11 - Monday, October 10, 2005
119
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
123
124
125v3.10 - Monday, October 3, 2005
126
127- ADDED: Support for IPLab file format
128- ADDED: Better support for Zeiss LSM, Metamorph STK and Fluoview TIFF
129
130- TWEAK: Quicker initial processing of multi-file datasets
131- TWEAK: More efficient image display in many cases (using ImageRendererJ3D)
132
133- FIXED: Disallow "In 3D" display option when Java3D is not installed
134
135
136v3.09 - Monday, July 25, 2005
137
138- ADDED: Ability to export data objects directly to ImageJ
139- ADDED: Folder chooser to export dialog for specifying which folder to use
140
141- TWEAK: Warn user if export to 24-bit RGB will truncate data values
142
143- FIXED: Ignore first image (pure white RGB) of Openlab datasets
144
145
146v3.08 - Tuesday, July 19, 2005
147
148- ADDED: Ability to specify pixel type for datasets uploaded to OME
149- ADDED: A command-line tool for uploading datasets to OME: "omeul"
150
151- FIXED: More robust visbio.tmp deletion on program exit
152
153
154v3.07 - Friday, July 15, 2005
155
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
159- ADDED: Option to configure eye separation distance
160
161- FIXED: Problem with eye separation in stereo mode
162
163
164v3.06 - Tuesday, July 12, 2005
165
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
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
172
173
174v3.05 - Friday, July 8, 2005
175
176- ADDED: Copy, paste and mass distribution overlay functions
177- ADDED: Initial implementation of MATLAB-VisBio interface
178
179- FIXED: Remove selected overlays only affects the current dimensional position
180- FIXED: Improper color summing when Java3D not present
181- FIXED: Problem adjusting maximum heap on Mac OS X
182- FIXED: Add loci-ome-xml.jar to launch scripts
183
184
185v3.00 final - Wednesday, June 8, 2005
186
187- ADDED: "Sample datasets" menu for automatically downloading sample data
188- ADDED: Ability to specify dataset's physical dimensions in microns
189- ADDED: More robust XML-based program states
190- ADDED: Options for controlling thumbnailing parameters
191- ADDED: Options for controlling image stack parameters
192
193- TWEAK: Option to toggle hiding of all windows when main window is minimized
194
195- FIXED: Subsampling image scaling bugs (relating to improper domain sets)
196- FIXED: Bug in image sequence capture when no file extension is given
197- FIXED: Disallow invalid combinations of stack settings
198- FIXED: Better subsampling error checking
199
200
201v3.00 beta5 - Tuesday, April 26, 2005
202
203- ADDED: Data export: save a data object to a file series on disk
204- ADDED: Ability to download images from an OME database (OME image transform)
205- ADDED: Dragging selected overlays with the pointer tool moves them
206- ADDED: Support for key/value pair command-line parameters
207- ADDED: Ability to launch VisBio through a web browser with Java Web Start
208- ADDED: Support for PNG images
209- ADDED: All online help topics are written
210
211- TWEAK: VisBio icon is now used instead of default Java cup icon
212- TWEAK: System property for controlling native frame decoration (for L&Fs)
213- TWEAK: Only one VisBio instance allowed to run at a time
214- TWEAK: Secondary instances pass parameters to active instance before quitting
215- TWEAK: Remove OME-CA XML state logic completely
216
217- FIXED: Several overlay bugs eliminated
218- FIXED: More robust behavior when Java3D is not installed
219- FIXED: More descriptive error messages if VisBio fails to start up
220- FIXED: Combo box width for Windows Look & Feel
221- FIXED: Lots of little bugfixes
222
223
224v3.00 beta4 - Wednesday, March 16, 2005
225
226- ADDED: Volume rendering
227- ADDED: Arbitrary slice data transform
228- ADDED: Data cache system for managing full-resolution data in memory
229- ADDED: Expanded VisBio help system
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
237
238- FIXED: Rewrote TIFF importer to be an order of magnitude more efficient
239- FIXED: Broken data transforms (sampling, max intensity, collapse, spectral)
240- FIXED: Upside down ZVI datasets
241- FIXED: Several overlay data transform bugs
242- FIXED: Several window centering issues
243
244
245v3.00 beta3 - Wednesday, February 2, 2005
246
247- ADDED: Overlays data transform for creating overlay annotations
248- ADDED: "Immediate" data transforms that ignore full-resolution burn-in delay
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
252- ADDED: Preload most classes to speed up VisBio response time
253- ADDED: Controls for altering how long full-resolution burn-in is delayed
254- ADDED: Ability to toggle whether consoles pop up when output is produced
255- ADDED: System button for dumping system properties to output console
256
257- TWEAK: Dataset chooser displays progress bar while analyzing file pattern
258- TWEAK: Dataset chooser jumps to directory specified in file pattern field
259
260- FIXED: Occasional multiple data transform burn-in deadlock
261- FIXED: A bunch more little bugfixes
262
263
264v3.00 beta2 - Wednesday, October 27, 2004
265
266- ADDED: Preliminary support for Zeiss LSM and ZVI file formats
267- ADDED: Continue work on comprehensive state support in XML format
268
269- FIXED: Mac OS X menu bar behaves much better
270- FIXED: Various other bugfixes and improvements
271
272
273v3.00 beta1 - Wednesday, September 1, 2004
274
275- ADDED: Support for Metamorph STK file format
276- ADDED: Support for Olympus Fluoview file format
277- ADDED: Support for Openlab LIFF file format (requires QuickTime for Java)
278- ADDED: Dimensional collapse transform
279- ADDED: Weighted multispectral component mapping transform
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
283
284- FIXED: Tons of bugfixes and improvements
285
286- TWEAK: Switched Windows distribution to ZIP file; no need for an installer
287- TWEAK: Windows distribution now defaults to "JGoodies Windows" Look & Feel
288- TWEAK: Linux distribution now defaults to "JGoodies Plastic 3D" Look & Feel
289- TWEAK: Fixed up all distribution packages
290
291-------------------------------------------------------------------------------
292v2.31 - Thursday, July 1, 2004
293
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)
297
298- FIXED: Long delay before first screen dataset is computed
299
300- TWEAK: Switched Windows installer to JSmooth + Inno Setup
301- TWEAK: Switched Linux distribution to a simple script file
302
303- GONE: Eliminated Solaris distribution
304
305
306v2.30d - Monday, June 14, 2004
307
308- FIXED: Bugs when Java3D is not installed
309- FIXED: Greatly improved burn-in function / slider responsiveness
310
311
312v2.30c - Tuesday, April 13, 2004
313
314- FIXED: Issue with "Open file" functionality
315- FIXED: Bug when nothing is mapped to Z-axis
316
317
318v2.30b - Tuesday, March 30, 2004
319
320- FIXED: Number doubling bug in file pattern detection logic
321
322
323v2.30a - Wednesday, February 18, 2004
324
325- FIXED: Minor data import bug
326
327- GONE: Old "import series" dialog box ("Import group" does everything)
328
329
330v2.30 - Monday, February 2, 2004
331
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
336
337- FIXED: Full-resolution burn-in bug with arrow buttons
338
339- TWEAK: Raised volume rendering limit to 192x192x192 pixels
340
341
342v2.21 - Thursday, January 15, 2004
343
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
347
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
353
354- TWEAK: Better status bar messages
355
356
357v2.20 - Monday, January 5, 2004
358
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
362
363- GONE: Previous/next preview displays
364
365
366v2.10 - Monday, December 15, 2003
367
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
370
371
372v2.04 - Friday, December 5, 2003
373
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
380
381- FIXED: Mac OS X Application menu items now work as expected
382
383
384v2.03a - Friday, November 21, 2003
385
386- FIXED: Deal with bugs preventing proper saving of QuickTime movies
387
388- TWEAK: Display positions on Capture tab list can now be given better names
389
390
391v2.03 - Wednesday, November 19, 2003
392
393- ADDED: Separate ij.jar, for upgrading ImageJ independently of VisBio
394
395- FIXED: Better QuickTime for Java detection on Windows XP
396
397- TWEAK: Better error messages when an error occurs during file import
398
399
400v2.02 - Monday, November 17, 2003
401
402- ADDED: Capture 3-D display sequences to QuickTime movie files
403- ADDED: Mac OS X version is now distributed as an application bundle
404
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
410
411
412v2.01 - Friday, September 5, 2003
413
414- ADDED: Undo is back, with multiple undo & redo support
415
416- FIXED: Many save & restore state bugs fixed
417- FIXED: Many measurement bugs fixed
418- FIXED: Various other bugfixes
419
420
421v2.00 - Friday, August 8, 2003
422
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 QTJava.zip
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
445
446- FIXED: Tons of bugfixes (and surely many new bugs--please report them!)
447
448- GONE:  Drift correction will be back with the next release
449- GONE:  Undo support will be back with the next release
450
451-------------------------------------------------------------------------------
452v1.0 beta 3C - Wednesday, October 30, 2002
453
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
458
459
460v1.0 beta 3B - Friday, October 11, 2002
461
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
468
469
470v1.0 beta 3A - Thursday, October 10, 2002
471
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
476
477- TWEAK: Improved thread usage relating to progress dialog
478
479
480v1.0 beta 3 - Friday, October 4, 2002
481
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
500
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., "GLASS20006292355.nc")
507- FIXED: Disallow 2-D standard measurement lines spanning multiple slices
508- FIXED: Rightmost value of color widgets can be properly manipulated now
509
510- TWEAK: Quit operation can now be canceled
511
512
513v1.0 beta 2A - Tuesday, August 27, 2002
514
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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