Phylum Release Notes
Stop-press Documentation
These release notes cover Phylum for both Windows and Macintosh.
Phylum versions 4.0 and above for Macintosh require Mac OS X 10.4.7 or above to function correctly.
Phylum versions 2.6 and above require Improvision License Server 1.1 or above.
Known Problems
It may not be possible to open library clippings created in Phylum 4.0 in earlier versions of Phylum.
Version History
Version 4.2.1 (21 November 2007)
Added support for Olympus ZDC autofocus system (FB11246)
Fixed problem that could occasionally cause artefacts when using Photometrics cameras (FB9786)
Fixed problem where deconvolving an empty image would cause an error - we now output an empty image (FB11311)
Fixed problem where multi-block deconvolution of very large datasets could stall on the last block (FB11341)
Fixed problem where NA values in measurement columns would not get sorted together (FB11345)
Fixed problem where older PVCAM cameras would not be correctly initialized
Fixed problem where Phylum could crash if invalid Neurolucida XML files are imported (FB11408)
Fixed problem where stamp ROI tool did not behave as expected on 3D images (FB11612)
Fixed problem where the scale bars would change length when "Show Axis Length" was turned on and off (FB11516)
Improved algorithm used for selecting point positions when tiling within a well on the XY stage view (FB11442)
Improved behavior when viewing measurement tables with hundreds of thousands of rows (FB11454)
Mac: Fixed problem where C9100-13 camera will time out acquiring background subtraction or shading images (FB11364)
Mac: Fixed problem where it was not possible to enter a decimal point into the ROI stamp tool dialog (FB11547)
Mac: Fixed problem where Phylum would hang when making a new library on Mac OS X 10.5 (Leopard) (FB11580)
Mac: Worked around Mac OS X bug that could cause a crash in the 3D view (FB11626)
Windows: Fixed problem where buttons would need to be clicked twice when a wizard window was up (FB11130)
Windows: Fixed problem where pressing the CTRL key in an edit field that should only accept numbers would then allow it to accept invalid characters (FB11446)
Windows: Fixed problem where print preview of an empty library would cause a crash
Windows: Fixed problem where text in "Make Volumes" dialog would be cropped (FB11399)
Windows: Improved error message when trying to save ROIs that are too large to be stored in the Windows registry (FB11613)
Version 4.2 (13 August 2007)
Added control over speed and acceleration for ASI stages (TT11107)
Added icon for TE2000 analyzer (TT11103)
Added support for bi-directional Z stacks (TT9332)
Added support for DCAM 3.0 and advanced capabilities of Hamamatsu C9100-13 camera (TT11041)
Added support for Improvision Acquisition Hub 2.0 (TT10739)
Added support for Leica LIF format version 2 (TT11151)
Added support for Nikon Perfect Focus System (TT10990)
Added support for reading and writing OME-TIFF (TT10751)
Added support for rotating the image from DCAM cameras (TT11193)
Added support for using auto-focus in single-point experiments (TT8928)
Fixed crash in Ratio dialog (TT11046)
Fixed crash on launch with Windows 2000 (TT11114)
Fixed error when joining tracks (TT11085, TT11112)
Fixed error with batch measurements with some measurement protocols (TT11106)
Fixed inconsistencies in menu items between Mac and Windows (TT11074)
Fixed inconsistencies in tool items between Mac and Windows (TT11086)
Fixed inconsistencies in tool tips between Mac and Windows (TT11062)
Fixed occasional crash in FRET dialog (TT11186)
Fixed problem that could cause deadlock with irregular ROIs in colocalisation view (TT11043)
Fixed problem where “Flip” tool was not working (TT11253)
Fixed problem where a piezo drive attached to the Acquisition Hub was not moved to the centre position on startup (TT11162)
Fixed problem where binning values in the Analysis view could not be set to less than 1.0 (TT11173)
Fixed problem where empty sequences could be added to the library if acquisition was stopped before the first timepoint is complete (TT11111)
Fixed problem where focus limits were not remembered for every focus drive type (TT11171)
Fixed problem where hiding tracks did not hide the track objects (TT11101)
Fixed problem where ROI stamp tool was using pixels when µm had been selected (TT11061)
Fixed problem where spatial calibration was not adjusted for binning changes on Photometrics cameras (TT11146)
Fixed problem where TE2000 analyzer would always be shown as being in the “in” state (TT11124)
Fixed problem where temporary files could be left in library folder (TT11036)
Fixed problem where track colors on charts would not match the colors of the original tracks (TT11047)
Fixed problem where using custom shape in a measurement protocol could cause an OpenGL warning (TT11026)
Fixed problem with default thresholds in colocalisation view (TT11042)
Fixed problem with error 13157 when changing Zeiss Axioplan TL voltage (TT11052)
Fixed problem with importing large Leica LIF files (TT11049)
Fixed problem with incorrect default channels being selected in batch measurements (TT11117)
Fixed problem with progress bars in background correction (TT11013)
Fixed problem with timestamp information in some Leica LIF files (TT11205)
Fixed problems where timestamp data could not be read for some STK files (TT11152)
Fixed problems with calibration information in some Leica LIF files (TT11158)
Improved auto-focus – last “good” focus is now always used as starting point for next auto-focus (TT11084)
Improved behavior when exporting floating-point images to TIFF (TT11181)
Improved memory management when measuring large sequences (TT11275)
Improved reliability when calibrating ASI XY stages (TT11247)
Mac: Fixed problem where ROI feedback opacity was not being honored correctly (TT11170)
Restored support for relative track position information (TT10960)
Windows: Fixed problem in image view where mouse scroll wheel would move two image planes for every click (TT11160)
Windows: Fixed problem where copy and paste did not work for some edit fields (TT11123)
Worked around problem with older Leica microscopes where the scope would report an RF4 turret was present when actually an RF8 turret was present (TT11165)
Version 4.1 (30 March 2007)
Added “Restore Objects” task for measurement protocols, this allows retained objects to be reused (TT10592)
Added “TIFF for Publication” file export filter – this exports images as “millions of colors” and avoids problems with LUTs and 16-bit source images (TT10479)
Added better icons for some video controls (TT10473)
Added photo-bleaching correction tool
Added ROI stamp tool, this allows ROIs of a defined shape or size to be repeatedly created (TT10854)
Added support for automatically opening shutters during auto-exposure (TT10834)
Added support for built-in Zeiss AxioImager XY stage (TT10661, IS20446, IS19220)
Added support for controlling Olympus DSU Spinning Disk unit (TT8055)
Added support for controlling speed and acceleration of Ludl XY stages (TT10607)
Added support for different scales in histogram displays – ctrl-click (Windows) or alt-click (Mac) will switch between them (TT10461, IS18396)
Added support for freezing the video preview (TT8297)
Added support for GE Healthcare XML/TIFF image format (TT10389)
Added support for grouping sets of objects in measurement protocols; this allows analyses that compare different object populations (TT10546)
Added support for integrated Optigrid controller with automated grid focus (TT10435)
Added support for measuring a PSF from a single-channel, single-timepoint image sequence (TT10822)
Added support for packed 12 bits/component TIFF files (TT10964, IS21593)
Added support for QImaging Rolera MGi (TT10467)
Added support for reading Neurolucida XML tracing files (TT10714)
Added support for Windows Vista (TT10510)
Added support for XY focus maps (TT9341)
Added support for Zeiss AxioObserver (TT10434)
Added support for Zeiss Axioskop 2 MOT Plus (TT10644)
Added support for Zeiss WSB Piezo XY Stage (TT10450, IS18248)
Added tool to video preview for moving XY stage to clicked point (TT10804, IS20919)
Added XY stage preference panel to centralize XY stage preferences (TT10945)
Fixed incompatibility between Phylum Live and Metamorph when using a Prior Proscan controller with both software packages (TT10422, IS17426)
Fixed inconsistencies with spatial calibration in the video preview (TT10603, IS19982)
Fixed intermittent crash with adding images to an image sequence (TT10614, IS20007)
Fixed internal error that could sometimes occur when sorting measurements (TT10645)
Fixed internal error with merging measurement items (TT10731, IS20386)
Fixed problem importing single Z, multi-channel Biorad PIC files (TT10778, IS20575)
Fixed problem where “Separate Touching Objects” could hang (TT10942, IS20608)
Fixed problem where an image sequence containing timepoints more than one year apart would not work properly (TT10657)
Fixed problem where aspect ratio of images from MicroPublisher 5.0 camera could be wrong (TT10934)
Fixed problem where auto-exposure could not be stopped (TT10600)
Fixed problem where background correction could produce unexpected results (TT10905, IS21359)
Fixed problem where canceling undo then canceling a process would cause the process to go ahead anyway (TT10777, IS20811)
Fixed problem where LMM-5 laser power meter would cause a lot of experiment log entries (TT10615)
Fixed problem where measurements table would scroll to the top when sorted (TT10671)
Fixed problem where red-green stereo rendering was not working properly (TT10483)
Fixed problem where some OIF files could be imported as black (TT10629, IS20328)
Fixed problem where switching serial ports that have already been allocated would not produce expected results (TT10650)
Fixed problem where the default scale in the “Change Size” dialog was zero (TT10948)
Fixed problem with dual-scan Hamamatsu cameras where the high bit-depth images could look corrupted (TT10883, IS21008)
Fixed problem with importing some Zeiss LSM files (TT10816, IS20791)
Fixed problem with multi-point acquisition where pause button would not pause until the end of the timepoint; we now pause at the end of the point (TT10543)
Fixed problems importing some Leica TIFF files (TT10775, IS10642)
Fixed problems importing some PerkinElmer UltraView files (TT10574, TT10693)
Improved behavior when dealing with invalid times (TT10634)
Improved calculation of black and white points for acquired Z stacks when auto-contrast is switched on (TT10620)
Improved icons in preference dialog (TT10379)
Improved importing of datasets that consist of many files in a folder – we now create a single image sequence rather than an image sequence in a folder (TT10692)
Improved measurement and ROI feedback – extensive options are now available (TT10480)
Improved performance of importing datasets that consist of many TIFF files (TT10692)
Improved performance of measurement tables with large numbers of measurements (TT10537)
Improved reading of LUT information from MetaMorph STK files (TT11015, IS21490)
Improved serial port configuration – we now lists ports and allow devices to be assigned to the port rather than listing devices and assigning ports to them, this reduces the clutter in this preference panel (TT10651)
Improved support for boolean operations in measurement protocols (TT9957)
Improved wording of “Change Colors” dialog (TT10630)
Mac: Added proxy icons to windows that are linked to files (TT11020)
Mac: Fixed cosmetic problems with the “Find Objects by Intensity” dialog (TT10619)
Mac: Fixed intermittent crash on quit (TT10742)
Mac: Fixed problem where text on “timeline” view was corrupted in Mac OS X 10.4.7 and up (TT10941)
Mac: Fixed problem where zooming in on the XY stage view could eventually cause an internal error (TT10752)
Moved to Metakit 2.4.9.6 (TT10674)
Windows: Fixed problem where clicking the “target” button in the Navigation palette for a channel that is already targeted would select the next channel (TT9454)
Windows: Fixed problem where large experiment logs could take a long time to open (TT10940)
Windows: Fixed problem where light paths could stop working after being edited by double-clicking them (TT10715)
Windows: Fixed problem where minimizing and maximizing the video preview window would sometimes cause the preview to stop (TT10857)
Windows: Fixed problem where running Phylum without acquisition would cause serial port settings to be lost (TT10680, IS20490)
Windows: Fixed problem where video preview could stop working if the computer was locked while the preview was running (TT10708, IS20508)
Windows: Fixed problem with white bands appearing at the top and bottom of AVI movies – the bands are now black (they cannot be avoided) (TT10858, IS20485)
Version 4.0.1 (17 Nov 2006)
Added missing support for copy to clipboard for measurements items (TT10445)
Added option to reverse the direction of the ORBIT 1 focus drive (TT10436)
Fixed a problem where measurement protocols could not be read from a file if no protocols were saved in the preferences (TT10502)
Fixed incorrect internal error if iterative restoration runs out of address space when re-assembling the final image (TT10189)
Fixed internal error if deconvolution is used on two channels in a sequence that both have the same name (TT10464)
Fixed problem importing some BioRad PIC files (TT10484, IS118850)
Fixed problem that could cause a crash when switching between image sequences of different lengths (TT10459)
Fixed problem where “Select None” and “Select All” menu items could be incorrectly enabled (TT10363, TT10400)
Fixed problem where “Separate Touching Objects” measurement task does not work on images with exactly two Z slices (TT10199)
Fixed problem where 3D rendering view would always show feedback for all timepoints regardless of the preferences (TT10401)
Fixed problem where a deadlock could occur if an ROI was repeatedly dragged around the video preview (TT10535)
Fixed problem where adding measurements to an existing measurements item could cause feedback to stop working for older rows (TT10376)
Fixed problem where binary operations measurement tasks would always use the first saved object set regardless of what was selected (TT10443)
Fixed problem where black and white point of deconvolved image could be reset if library was closed and then opened again (TT10504)
Fixed problem where changing image depth from 16-bit greyscale to millions of colors could result in a white image (TT10456, IS18811)
Fixed problem where colocalization measurement tasks could return error 2500 (TT10499, IS19212)
Fixed problem where copying a region in the “extended focus” image view would cause an error (TT10495, IS19305)
Fixed problem where default upper limit in “Find Objects by % Intensity” measurement task would not be 100% (TT10524)
Fixed problem where disabling channels in 3D view could cause artifacts (TT10545)
Fixed problem where feedback would disappear when timepoints are switched (TT10469, IS18782)
Fixed problem where hiding columns in the measurements table could prevent rows from being selected (TT10438)
Fixed problem where illumination correction would not work on single images (TT10522)
Fixed problem where incorrect calibration values could be used when processing single images (as opposed to image sequences) (TT10462)
Fixed problem where initial iteration in restoration could be extremely slow (TT10442, IS18529)
Fixed problem where iso-surface renderer would be incorrectly enabled for color channels (TT10482)
Fixed problem where page up and page down did not always move the Z plane in the image view (TT10406, IS18228)
Fixed problem with importing Olympus FluoView files (TT10423, IS18298)
Fixed problem with reading calibration information from Leica .LIF files (TT10428)
Fixed problems importing some .LEI files (TT10410, TT10425, TT10453, IS18124, IS18709)
Fixed problems importing some LIFF files (TT10440)
Fixed problems importing some PE UltraView files (TT10411, TT10521, IS18124, IS19628)
Improved compatibility with other applications by resetting the Proscan controller back to its default mode on exit (TT10422, IS17426)
Improved ICS import to include emission wavelength information (TT10542, IS19681)
Improved page-by-page scrolling in tables (TT10398)
Improved support for older Zeiss AxioPlan TL lamps (TT9299)
Improved video frame rates in XY stage view (TT10544)
Improved wording in “Separate Touching Objects” measurement task (TT10523)
Line tool now reads out in µm rather than voxels (TT10441)
Mac: Fixed problem where setup for fast restoration would keep changing when the dialog was opened (TT10489, IS19239)
Mac: Fixed problem with installer where plugins could not be disabled (TT10420)
Mac: Fixed problems where splitters in views could be dragged off the bottom of the view (TT10414)
Mac: Fixed small drawing glitch at the top of the measurements view (TT10397)
Mac: Fixed some cosmetic issues in the measurements view (TT10413, TT10417)
Mac: Using page up and page down in a table no longer changes the selection (TT10399)
Windows: Fixed error 122 in Japanese version of Windows (TT10485, IS18705)
Windows: Fixed problem where changing the color of a sequence would not update the color of the examples in the controls (TT10382)
Windows: Fixed problem where Ludl XY stage setup dialog would not accept decimal points (TT10501)
Windows: Fixed problem where SMA unlock codes could not be processed (TT10419)
Windows: Fixed inconsistent behavior of mouse wheel in image view (TT10446, IS18396)
Version 4.0 (29 Sep 2006)
Added “Color Balance” dialog – this replaces the “Levels” dialog (TT9435)
Added “Contrast Enhancement” dialog – this replaces the “Levels” dialog (TT9434)
Added “maximum intensity over time” graph to feedback in Video Preview window - this is designed to show whether samples are bleaching or not (TT9186, TT9774)
Added “Measurements” view – this forms part of the new Quantitation module that replaces Classification (TT9433)
Added “Raw” view for measurement items - this forms part of the new Quantitation module that replaces Classification
Added a “Z Step” property. This contains the original mechanical step used for acquiring the data (TT8746)
Added Background Correction module (TT8675)
Added Registration Correction module (TT8600)
Added support for “laser line” devices (TT8844)
Added support for adjusting Z positions of XY points while a multi-point timelapse is running (TT8659, IS11323)
Added support for batch processing to many tools (TT8714)
Added support for changing Bayer interpolation modes on QImaging cameras (TT9742, TT10036)
Added support for customizing the Z range for piezo focus drives driven from the Improvision Acquisition Hub – this allows the Hub to be used with focus drives from more manufacturers (TT9524)
Added support for different 16-bit image types in DeltaVision files (IS15206, TT9610)
Added support for integrated TL shutter on Zeiss Axiovert microscopes (TT8814)
Added support for labelling light path icons with arbitrary text (TT7767)
Added support for Leica DMIRBE microscope (TT10015, IS15382)
Added support for Leica LIF file format (TT8800)
Added support for LMM-5 laser excitation system (TT9187)
Added support for manual actions when changing light paths - this makes it easier to use Phylum with manual microscopes (TT8840)
Added support for Nikon E1000 microscope (TT9235)
Added support for Nikon TE2000 motorized analyzer (TT8871)
Added support for pausing acquisition (TT8601, TT8394)
Added support for QImaging Retiga SRV camera (TT8868)
Added support for saving and restoring ROIs (TT9025)
Added support for undoing ROI changes (TT9298)
Added support for using joypads to navigate in the 3D view (TT8959)
All numerical edit fields are now right aligned (TT7950)
Black level in “Rendering” view now uses a log scale to give finer control closer to zero (TT8635)
Changed name for “Spinning Disk” PSF to “Spinning Disk CSU10/CSU22” (TT7110)
Changed servo activation distance for Ludl stepper stages to 1 – this improves positioning reliability for these stages (TT9078)
Changed shortcut for “Switch to Live Video” from Control-Shift-L (Windows) or Command-Shift-L (Mac) to Control-Shift-V (Windows) or Command-Shift-V (Mac) to prevent conflict with “Levels” dialog (IS14279, TT9210)
Fixed inconsistencies between Mac and Windows in the ordering of menu items (TT9622)
Fixed problem that could cause a corrupt image sequence if data was added to the sequence and then the add was undone (TT9226)
Fixed problem where editing channel timings in the acquisition setup dialog could reset the light paths for the channels (IS13710, TT9075)
Fixed problem where error 1252 could sometimes be erroneously reported (TT8441)
Fixed problem where exporting images as Windows BMP was very slow (IS14295, TT9421)
Fixed problem where interrupting the save of a QTVR file would leave the file open in an inconsistent state (TT10119)
Fixed problem where iterative restoration could leak memory in “block” mode if paused and restarted at certain points (TT8681)
Fixed problem where overwriting one file with another could sometimes leave data from the original file in the new one (TT9494)
Fixed problem where preferences were not correctly taking byte order into account (TT9199)
Fixed problem where saving measurements over the top of an existing file would not overwrite the file properly (TT9494)
Fixed problem where skeletal diameter for 2D image could be reported as 0 (TT9367)
Fixed problem where skeletal diameter of a 2D object could be incorrectly reported as 0 µm (TT9367)
Fixed problem where slice view progress could become “stuck” if views are switched while it is processing (TT8676)
Fixed problem where track times were not based on object times – they are now given the time of the first object in the track (TT9048)
Fixed problem where trying to acquire 0 timepoints in the “Video Preview” window would cause a hang (TT10121)
Fixed problem where undoing a “crop” operation would reset the color of the image (TT9593)
Fixed problem where using “Capture Snapshot” on a chart could cause an error (IS14929, TT9485)
Fixed problem where using multiple DCAM cameras could cause devices to interfere with each other (TT9999)
Fixed problem with Axioplan 2ie microscopes where the “oil stop” feature would cause Phylum to time out when moving between objectives (TT9189, IS13854)
Fixed problems with “Change Size” dialog that could cause calibrations to become zero or infinite (TT9981)
Fixed problems with auto-scroll in the image view (TT9654)
Image sequences from multi-well experiments are now labelled properly with the well description (TT9339)
Improved behavior of “lasso” ROI tool (TT9590)
Improved behavior of freehand and circular ROI tools when zoomed in on the image (TT9505)
Improved file export – it is now possible to export image sequences and 3D images directly to a TIFF file or movie (TT9662)
Improved file import – where possible files are imported directly to an image sequence, this improves both usability and speed (TT9244, TT9622)
Improved icons for exported clipping and settings files (TT9942)
Improved importing of PE AIC files (TT9568)
Improved layout of “Change Size” dialog (TT9982)
Improved performance when acquiring images at a large number of XY points (TT9343)
Improved reading of BioRad PIC metadata (channel colors and white point) (TT9201, IS14253)
Improved scanning of randomly placed XY points – we now try and find an optimal path between the points (TT9897)
Improved speed of importing BioRad PIC files (TT9200, IS14218)
Improved speed of importing Openlab LIFF files (TT8958, IS13031)
Improved startup screens – user is no longer asked for registration details, if no hardware key is found a new dialog makes it easier to understand what to do (TT9406)
Improved string sorting – strings containing numbers are now sorted “naturally”, e.g. “My cat has 3 legs” will be sorted before “My cat has 10 legs” (TT9995)
Improved track charts – this chart now uses the calibrated centroid position of each object in µm rather than the uncalibrated position in voxels (TT9905, IS15758)
Improved XY “scan area” feature – we now overlap the scans slightly to prevent “seams” appearing (TT8728)
Lowered value used for “Low” and “Lowest” resolution limits in 3D preferences. This improves performance for large datasets (TT9285)
Mac: Added support for “universal” DCAM drivers that support both PowerPC and Intel Macs (TT9873)
Mac: Added support for “universal” QImaging drivers (version 2.0) that support both PowerPC and Intel Macs (TT10004)
Mac: Fixed crash changing brightness when playing through an image sequence (TT9606)
Mac: Fixed problem where “Hide Toolbar” command did not always reflect the current state of the toolbar (TT9499)
Mac: Fixed problem where menu items in the “Video Preview” window would become disabled after making a well overlay (TT9909)
Mac: Fixed problem where wrong timepoint could be checked in “timepoint” popup (TT10104)
Mac: Navigation palette “timepoint” popup menu is now consistent with Windows and allows 200 timepoints before it is disabled (TT10088)
Mac: Phylum now uses the built-in Mac OS X installer (TT10277)
Mac: Improved behavior of popup color menus – they now support “sticky” menu mode as well as “click and hold” (TT8734, IS11648)
Mac: Improved drawing of “header” panes on some views (TT8555)
Mac: Phylum 4.0 is a universal (Intel and PowerPC) application
Mac: Added support for mouse scroll wheel (TT8543)
Mac: Fixed crash switching to 3D view with some datasets (IS14970, TT9507)
Mac: Fixed problem that could cause a crash if an error occurred during acquisition (IS14421, TT9289)
Mac: Fixed problem where “Print Preview” did not work for 3D view (IS14943, TT9430)
Moved PSF creation menu items to "Create New" menu (TT8620)
Option to “break image into blocks” is now always enabled in restoration dialogs - this is less confusing (TT8916, IS12716)
Removed “Classifier” module, changed “Measurements” module so it could display old measurements but not create new ones.
Single images captured from the “Video Preview” window now have the light path name included in their name where a light path is selected (TT9314)
Windows: Fixed problem that could cause a crash if a QImaging camera was unplugged while it was in use (TT10045)
Windows: Fixed problem where double-clicking an ROI tool did not select the whole image (TT9828)
Windows: Fixed problem where entering a “.” into fields in the “Slice” view could cause a hang (TT10113)
Windows: Fixed problem where it was only possible to draw lines of a single color on 2D images (TT9319, IS14633)
Windows: Fixed problem where scroll bars could disappear from the “Library” window under some circumstances (TT10147)
Windows: Improved error message if QuickTime features are used when QuickTime is not installed (TT9495)
Windows: Improved layout of PSF dialogs (TT9989)
Windows: Windows XP Service Pack 2 or Windows 2000 Service Pack 4 are required to install Phylum (TT9407)
Windows: Fixed hot tracking on measurements table header (TT8541)
Windows: Improved “selected” state for buttons to make it clearer (TT7981)
Windows: Added support for light path control on Nikon 90i (TT9717)
Windows: Added support for motorized analyzer on Nikon 90i (TT9718)
Windows: Added support for multiple Nikon 90i microscopes – this is required for the fluorescence head unit to work properly (TT9351)
Windows: Fixed problem changing line colour on image view – sometimes the colour would not change reliably (IS14633, TT9319)
Windows: Fixed problem where dragging an item into a linked folder does not cause an error (TT8799)
Windows: Fixed problem where minimising and then restoring the video preview window causes the timelapse acquisition rate to change (IS13922, TT9181)
Windows: Fixed problem where switching between “All Timepoints” and “Current Timepoint” in the “Measure Objects” dialog would reset the criteria to be measured (TT9170)
Windows: Fixed problem where toolbar buttons could go blank during a long session (IS14909, TT9470)
Windows: Phylum now requires a processor that supports SSE (e.g. Pentium III or better)
Worked around problem with Bayer QImaging cameras where image could turn purple when cropped (TT9066)
Worked around problem with Leica DM4000B microscope firmware where changing contrast modes could fail (TT9916, IS15335)
Version 3.7 (28 April 2006)
“Clear All Points” in “Video” menu is now available from both Live Preview and XY Stage views (TT8889)
Added recording of light path description in experiment log (TT8986, IS13270)
Added support for controlling the transmitted light voltage on the AxioVert 200M (TT8856)
Added support for Ludl MAC2000 (TT8880)
Added support for Ludl Piezo Z insert – this device must be configured with ID “Z” (6) (TT8960)
Added support for Nikon TIRF shutter system (TT8193)
Added support for Openlab 5 LIFF format (TT8946)
Added support for Zeiss AxioPhot 2 head (TT8934)
Added support for Zeiss MCU28 X-Y stage (TT8879)
Default iteration limit for Restoration is now 25 instead of 1 (TT9069)
Experiment Log view is now always available (TT8068)
Fixed crash during acquisition if changing light path causes control list to change (TT9040)
Fixed crash if the focus drive used by live restoration is unexpectedly removed (TT8832)
Fixed problem where adopted images sometimes cannot be exported (TT8896, IS12449)
Fixed problem where calibration information was not being read from STK files (TT8953)
Fixed problem where centroid calculations could be off by 0.5 pixels for simple rectangular objects (TT8808)
Fixed problem where focus drive and XY position displays would not display a “,” for the decimal point on European systems (TT9006, TT9007)
Fixed problem where importing some LSM files could cause error 1006 (TT8802, IS11916)
Fixed problem where Ludl MAC5000 could sometimes fail to initialise (TT9014, IS13219)
Fixed problem where older acquisition protocols could fail to restore (TT8897, IS12614)
Fixed problem where PE files with zero calibrations could cause an internal error (TT8964)
Fixed problem where progress on remove noise of many small images would never complete (TT8831)
Fixed problem where TL shutter on DMI6000B would not close properly (TT8999, IS13209)
Fixed problem where Zeiss AxioImager sideport names could be incorrect (TT8943, IS12982)
Fixed problem with AxioImager where selecting PH mode would actually select DIC (TT8801)
Fixed problem with movie sequencer where some combinations of brightness tasks could cause unexpected results (TT8938, IS12882)
Fixed problem with movie sequencer where some combinations of rotates could cause the object to flip between rotations unexpectedly (TT8819, IS12153)
In acquisition, Z focus drive now returns to its initial position before auto-focussing if two Z drives are being used (TT9031, IS13455)
Reduced logging of device attach/detach events – they could overwhelm the session log and slow the system to a crawl (TT9059)
Mac: Fixed problem where focus drive “set top” and “set bottom” dialogs would not accept non-integer values (TT8846)
Mac: Fixed problem where turning channels on or off in the 3D view could eventually cause a crash (TT8836, TT8852, IS12388)
Mac: Fixed problem with binning control that could cause it to change two levels rather than one (TT8803)
Mac: Fixed problem with color picker in light path setup dialog (TT8834, IS12191)
Mac: Fixed problems with libraries being served from AFP file servers (TT8963, IS12944)
Windows: Fixed auto-scroll for drag-and-drop in project and gallery views (TT8811)
Windows: Fixed problem where docked palettes could not be resized unless application window was resized first (TT8810)
Windows: Fixed problem where Nikon 90i digital head on 80i stand would not work properly (TT8821, IS11971)
Windows: Fixed problem where scrollbars could disappear from library view (TT8884)
Windows: Fixed problem where tool tips on navigation palette would move around unexpectedly (TT8882)
Windows: Fixed problem where using large numbers of Classifiers would cause strange behavior (e.g. disappearing icons) (TT9037)
Windows: Fixed problem where video view menus would be left in the menu bar after the video view is closed (TT9045)
Windows: Fixed problem with incorrect selections in project view (TT8807)
Windows: Improved handling of errors from Acquisition Hub (TT9065, IS13317)
Windows: Session log is now printable (TT8932)
Version 3.6.1 (28 November 2005)
Added explicit warning which will appear if the Optigrid does not move at all during calibration (TT8581)
Added shortcut keys for “Levels” and “Auto Contrast” dialogs (TT8490)
Added support for Nikon Remote Focus Attachment (TT8654)
Added support for Prior Proscan XY stage (TT8642)
Added support for user-defined delays for Improvision Acquisition Hub shutters (TT8749)
Corrected text in “Registration” preferences (TT8739)
Fixed crash that could happen if “Live Restoration” was used without a focus drive being present (TT8651)
Fixed hang in acquisition (TT8649)
Fixed potential crash in 3D view (TT8572)
Fixed potential crash that could occur if the 3D view is opened and closed several times (TT8656)
Fixed potential hang in video acquisition (TT8491)
Fixed problem that could cause a crash if a movie sequence is played and a window was open that had never been switched to the “3D” view (TT8655)
Fixed problem where “Remove Noise” could fail to work if the library had been created on a different platform (TT8610)
Fixed problem where an excessive number of events could be logged in the experiment log (TT8682, IS11345, TT8723)
Fixed problem where creating long movies in the 3D view could cause an out-of-memory error (TT8701)
Fixed problem where having two Classifiers with the same name could cause the wrong Classifier to be used for measurement (TT8716)
Fixed problem where importing an alias to a file would hang the application (TT8595)
Fixed problem where Iterative Restoration using “blocks” could still run out of memory (TT8574)
Fixed problem where setting the brightness of a channel to zero in the movie sequencer does not entirely remove it from the scene (TT8624)
Fixed problem where some Olympus microscope could report errors when moving the filter turret (TT8621)
Fixed problem where the navigation slider would not update when viewing a sequence that is being acquired (TT8660)
Fixed problem where using two Hamamatsu or QImaging cameras would not work properly (TT8639)
Fixed problem where Phylum could hang playing back a sequence in “play and stop” mode (TT8599)
Fixed problem where Phylum libraries could be damaged if the hard disk became full (TT8781)
Fixed problem with resampling timepoints to a new sequence (TT8627)
Fixed problems calibrating Leica DMSTC stage (TT8636)
Improved behavior of Hamamatsu Phoenix-attached Orca cameras (TT8646)
Improved behavior when setting zero on a focus device – the top and bottom marks are now adjusted to make sure they are within the valid range for the focus device (TT8663)
Improved efficiency of image sequences – they now take up less disk space, particularly for short sequences (TT8661)
Improved performance of rendering in low memory situations (TT8532)
Mac: Added support for Unsanity smart crash reporter. This allows crash reports to be sent directly to Improvision (TT8608)
Mac: Corrected spelling of “QuickTime” in QTVR dialog (TT8794)
Mac: Fixed crash playing through a sequence as it is being acquired (TT8688, IS11397)
Mac: Fixed problem that could cause a crash in “Remove Noise” (TT8596)
Mac: Fixed problem that could cause an internal error switching between “XYZ Planes” and “Extended Focus” in the image view (TT8602)
Mac: Fixed problem where buttons with popup menus were not drawing their popup arrows (TT8550)
Mac: Fixed problem where creating a line in the “Image” view and then moving between timepoints could cause an internal error (TT8570)
Mac: Fixed problem where creating QTVR movies could fail (TT8640, IS11205, IS11206)
Mac: Fixed problem where cropping an image would not be honoured immediately in the 3D view (TT8565)
Mac: Fixed problem where current source in “Source” menu in video preview was not checked (TT8684)
Mac: Fixed problem where gain on Hamamatsu C7780 is always set to 2 when opening the video preview (TT8774)
Mac: Fixed problem where Hamamatsu cameras could stop working if Phylum was started with the camera switched off (TT8766)
Mac: Fixed problem where the “QuickTime” slider in the “Levels” dialog was not drawing properly (TT8549)
Mac: Fixed problem where the version number was not being displayed on the “About…” box (TT8665)
Mac: Fixed problem where unplugging an Orca ERG camera while it is running could cause a crash (TT8742)
Mac: Fixed problem where Phylum could use 100% CPU time with some image tools (TT8538)
Mac: Fixed problem where XYZ planes in “Image” view could not be made to spin (TT8778)
Mac: Fixed problem with latest DCAM drivers that could prevent rendering views from being registered (TT8710)
Mac: Fixed problem with latest DCAM drivers that could prevent the DCAM camera from being registered (TT8667)
Mac: Improved performance of drawing in the “Image” view (TT8571)
Windows: Fixed crash opening some types of BMP file (TT8772)
Windows: Fixed memory leak in “Levels” dialog (TT8547)
Windows: Fixed missing text in “Registration” and “3D” preferences (TT8743)
Windows: Fixed problem where calibration tool in video preview could be a bit “jumpy” (TT8593)
Windows: Fixed problem where color ramp below histograms was not drawn correctly (TT8559, TT8560)
Windows: Fixed problem where library windows would sometimes not be displayed properly if another window is maximised when the library was opened (TT8759)
Windows: Fixed problem where playing through a sequence at high speed can be difficult to pause (TT8606)
Windows: Fixed problem where the video preview could stop updating if closed and reopened (TT8187, IS09893)
Windows: Fixed problem where the voxel spy would fail to update on a cropped video preview (TT8592)
Windows: The movie sequencer now scrolls automatically when playing to keep the “current” frame in view (TT8668)
Version 3.6 (31 August 2005)
Added button for “measure” to the “Classifier” palette (TT8282)
Added color reference to image view (TT8142)
Added support for automatically detecting and configuring objective and filter information for the Zeiss AxioImager microscope (TT8504)
Added support for breaking up fast and iterative restoration into blocks – this improves deconvolution times for a small decrease in quality (TT7843)
Added support for case-insensitive sort when sorting by item name (TT8340)
Added support for controlling motorized beam-splitter and Optovar on Zeiss AxioImager microscopes (TT8372)
Added support for directly entering microns-per-pixel in video calibration dialog (TT7623)
Added support for Leica DMSTC XY stage (TT8245)
Added support for MIP rendering (TT8149)
Added support for Photometrics PVCAM cameras (TT8050)
Added support for printing the slice view (TT8096)
Added support for Prior Proscan filter, shutter and Z controllers (TT8327)
Added support for rainbow display of monochrome images (TT8107)
Added support for Sutter 10-2 filter/shutter controller (TT8167)
Devices in the “serial ports” preference panel are now sorted by name (TT8281)
Fixed problem where “Create New / Open” dialog was using Volocity icons (TT8205)
Fixed problem where auto-focus results could very with focus position (IS09880, TT8249)
Fixed problem where cloaked, linked items in a library would become uncloaked when resolved (TT8460)
Fixed problem where creating a QTVR movie with pan or tilt set to 0 steps could fail with error –2014 (TT8198)
Fixed problem where DCAM cameras could sometimes issue a frame that was exposed before hardware had finished moving (TT8174)
Fixed problem where it could sometimes not be possible to switch between image sequences using the up and down arrow toolbar buttons (TT8279)
Fixed problem where ORBIT 1 focus drives could move incorrectly if the absolute position of the drive was large (IS10190, TT8320)
Fixed problem where turning off live restoration during an acquisition would cause the video preview to stop updating (TT8477)
Fixed problem where undo and then redo remove noise would not work correctly (TT8431, IS10455)
Fixed problem with hardware shaders that could cause a crash when hiding or showing channels (TT8386)
Improved behavior for showing warning in restoration dialogs if one or more images do not have any calibration information – the warning is now shown once with additional information logged in the session log (TT8349)
Improved colors on XY stage display to make them easier to see (TT8275)
Improved consistency of frame rates when acquiring video and opening shutters (TT8202)
Improved focus drive behavior for older Zeiss Axioplan microscopes (TT8383, IS10302)
Improved labelling of wells in XY stage view – they are now labelled A1, A2, A3 … B1, B2, B3 etc. This better reflects the labelling on well plates (TT8274)
Improved OptiGrid calibration – the calibration now more reliably finds an ideal result first time (TT8382)
Increased timeouts for Leica objective turrets (TT8212)
Mac: Fixed problem that could cause 100% CPU usage when the focus slider was visible (TT8471, IS10474)
Mac: Fixed problem that could cause a crash if Phylum ran out of memory (TT8438)
Mac: Fixed problem that could cause an internal error when switching to the extended focus view (IS09896, TT8221)
Mac: Fixed problem where “XYZ” view would not appear when printing image view (TT8302)
Mac: Fixed problem where cancelling Ludl device setup dialogs could cause the preferences to close (TT8371)
Mac: Fixed problem where measuring items during acquisition could fail (TT8287)
Mac: Fixed problem where menu items in the Video Preview window could become greyed out incorrectly (TT8223)
Mac: Fixed problem where print dialog would display page range of 9999 or 32767 in print dialog (TT8301)
Mac: Fixed problem where scale bars and other overlays were not being printed (TT8300)
Mac: Fixed problem where the summary text in the light path dialog could be clipped (TT8316)
Rendering view has been renamed to “3D” and supports multiple renderers (TT7689)
Simplified Classifier dialog to make it smaller and clearer, improved links between measurements and Classifier (TT8143)
Windows: Fixed problem where it was not possible to draw a freehand ROI if the drawing started in a direction between 12 and 3 o’clock (TT8430)
Windows: Fixed problem where the Voxel Spy palette would not scroll properly if a sequence had many channels (TT8445)
Windows: Updated HASP dongle drivers to latest version (TT8507)
Windows: Fixed problem that could cause a crash when auto-contrasting an image that contains only a single intensity (TT8375)
Windows: Fixed problem that could cause XY stage view to refresh incorrectly (TT8332)
Windows: Fixed problem that could very occasionally cause an internal error when dragging scrollbars (TT8330)
Windows: Fixed problem where an extra “.res” file could be created with QTVR movies (TT8222)
Windows: Fixed problem where an internal error could occur when charting very short sequences (TT8289)
Windows: Fixed problem where an internal error could occur when docking or undocking a palette from the application window (TT8247)
Windows: Fixed problem where Classifier palette would not be made scrollable until resized (TT8284)
Windows: Fixed problem where columns could not be reordered in chart data view (TT8334)
Windows: Fixed problem where dragging image sequence segments was broken (TT8331)
Windows: Fixed problem where image view crosshairs could be left on the image (TT8186)
Windows: Fixed problem where last digit of the time display could be clipped at the edge of the view (TT8260)
Windows: Fixed problem where maximised views would not always be sized properly (TT8325)
Windows: Fixed problem where movie sequencer playback speed would always be “fastest” unless the speed control is adjusted (TT8258)
Windows: Fixed problem where palette controls could disappear if the “return” key is pressed (TT8169)
Windows: Pressing the “return” key after changing an exposure value will now commit the change (TT8208)
Worked around problem where the focus drive on older AxioPlan microscopes would not move reliably (IS10302, TT8383)
Worked around problem with 16-bit STK files where some files would fail to import with error 1255 (IS09827, TT8211)
Worked around Zeiss AxioImager firmware bug where the microscope would report that it had completed a contrast mode switch before the movement was actually complete (TT8412)
Worked around Zeiss AxioImager firmware bug where the microscope would report that a focus move was complete when in fact it was not. This would cause the focus to drift during live restoration (TT8486)
XY stage wells are now scanned in a serpentine pattern to improve performance (TT8276)
Version 3.5.1 (10 June 2005)
Added support for auto-focusing once for each well when using an XY stage in multi-point experiments (TT8045)
Added support for creating a matrix of points centered on each well in the “XY Stage” view (TT8043)
Added support for double-clicking the preview in the “XY Stage” view – the stage will be moved to centre the clicked point (TT8044)
Added support for latest version of Zeiss LSM file format (TT8071)
Added support for moving the video preview within the “XY Stage” view – the preview can now be dragged to any corner (TT7871, TT8044)
Added support for reading and writing additional metadata in TIFF files (TT7951)
Added support for reviewing points and adjusting focus in the “XY Stage” view (TT8046)
Added support for saving and restoring well overlays and scan patterns in the “XY Stage” view (TT8041)
Added support for scanning points in the “XY Stage” view (TT8042)
Correct output depth is now given for DCAM cameras in the “Depth” popup control – before the options were 8-bit and 16-bit, now they are 8-bit and 12-bit (or whatever is appropriate for the camera) (TT7830)
Decreased speed of calibration for Ludl XY stages – this was causing stalls on some stages (the stage would make a beeping noise and fail to calibrate) (TT8110, IS09355)
Fixed incorrect interpolation warning that could sometimes appear when using Iterative Restoration (TT8117, IS09556)
Fixed problem where ORBIT 1 focus drive would not move accurately (TT8136)
Fixed problem where selection tools did not quite select as expected if the image was zoomed in (TT8029)
Fixed problem where sub-array was not being honoured properly and was therefore not producing the expected frame rate increase (TT8104)
Fixed problems with Leica DMRXA2 and DMIRE2 microscopes not being recognised reliably (TT8088)
Fixed problems with redrawing the timeline in the “Image Sequence” view while video is being acquired (TT7633)
Improved behavior of “Fast Restoration” for live video – the focus drive should no longer drift (TT8000, TT8033)
Improved error message when a user attempts to move an encoded Zeiss Axioimager objective from within Phylum (TT7817)
Improved reliability of ASI focus drive and stage (TT8032)
Mac: Added missing label for “filter” field in “Experiment Log” view (TT8099)
Mac: Fixed internal error that could eventually occur after switching between views many hundreds of times (TT8126)
Mac: Fixed problem where acquisition controls could be greyed out after accessing a dialog from the Video Preview window (TT7506, TT8048)
Mac: Fixed problem where it was impossible to dismiss or click on dialogs that appeared if an error occurred during an experiment (TT8132)
Mac: Fixed problem where the Voxel Spy readout would change in the middle of each pixel rather than at the edges if the image was zoomed (TT8016)
Mac: Fixed spurious error when exporting a QTVR movie on Mac OS X 10.4 (TT8114)
Mac: Removed performance enhancement that could potentially be causing library corruption (TT8105)
Mac: Worked around Mac OS X 10.4 bug where Altivec optimisations would be disabled on the G5 – this drastically affected the speed of Iterative Restoration (TT8085)
Windows: Fixed problem where editing names in the “library” view did not work properly (TT8098)
Windows: Fixed typo in Ludl shutter timing dialog (TT8070)
Version 3.5 (9 May 2005)
Added new icons for different filter changer types (excitation, emission, cube and ND) (TT7766)
Added support for a delay after opening or closing Ludl shutters (TT7429, TT7617)
Added support for ASI XY stages
Added support for Leica DM6000B built-in XY stage
Added support for locales – this means that we now properly honor regional settings such as decimal point characters and time formats (TT7648)
Added support for Ludl XY stages (TT7561)
Added support for Olympus FluoView OIF format (TT7215)
Added support for ORBIT 1 filters, shutters and focus drive (TT7711)
Added support for QImaging Micropublisher cameras
Added support for QImaging Retiga 2000R camera
Added support for reading PerkinElmer files with calibrations in nm instead of µm (TT7761)
Added support for setting µm per step for Ludl focus drives (TT7580, TT7618)
Added support for TILLVision DBB and .rbinf file formats (TT7326)
Added support for XY stages and multi-point acquisition (TT7345)
Added support for Zeiss AxioImager Z1 microscopes (TT7357)
Advanced Image Tools module now requires an unlock code (TT7598)
Changed cursor for video calibration line tool from a pointer to a crosshair (TT7889)
Errors in acquisition (e.g. unable to auto-expose) are now reported in an alert to make it clear to the user why acquisition was stopped (TT7743)
Fixed a problem where repeatedly duplicating samples could cause Phylum to lock up (TT7957)
Fixed crash if “Track Objects” was selected with only one timepoint hilited (TT7606)
Fixed problem that could cause a crash if you tried to delete a classifier but cancelled the delete (TT7686)
Fixed problem that could cause a crash when tracking (TT7643, IS08411)
Fixed problem that could cause a crash when using the lasso tool (TT7666)
Fixed problem that could cause an error if a PSF was generated while the video preview window was open (TT7582)
Fixed problem that could cause an error when reslicing a volume (TT7679)
Fixed problem that could cause incorrect classification if “Separate Objects” is selected and size thresholds have been set (TT7663, IS08478)
Fixed problem that could cause levels in movie sequence to never reach their maximum values (TT7866)
Fixed problem that could prevent images being displayed in “extended focus” mode with a read-only library (TT7677)
Fixed problem where “Undo Crop” would not work on image sequences (TT8028)
Fixed problem where acquisition protocol description would not update if Z top or bottom was changed but the Acquisition Setup dialog was not opened (TT7891)
Fixed problem where calibration properties would not be retained in resliced image (TT7825, IS08678)
Fixed problem where Fast Restoration preview does not update when restoration is complete (TT7610)
Fixed problem where invalid characters in item names (e.g. “ or / or \) could prevent items being exported (TT7645)
Fixed problem where light path settings would not update when you go to edit the path (TT7637)
Fixed problem where live restoration could cause the focus drive to gradually drift in one direction (TT8000)
Fixed problem where resolution of Retiga EXi camera would be incorrectly reported (TT7699)
Fixed problem where Slice View would not show same scale units as HR Rendering view (TT7608, IS08376)
Fixed problem where stopping acquisition while a light path was changing could cause Phylum to get into an inconsistent state (TT7589)
Fixed problem where the “offset” and “gain” icons were reversed on the Mac (TT7665)
Fixed problem where the light path buttons would not always reflect the current light path after an acquisition had finished (TT8013)
Fixed problem with auto-exposure tool that could fail to cause an error to be generated for an image that is too dark (TT7752)
Fixed range for QImaging QICAM offset control (TT7752)
Fixing problem where video zoom would not be remembered when video preview window is closed (TT7621)
Improved “Properties” dialog – items no longer get default properties, instead the property is left blank (TT7793)
Improved button icons in Slice View (TT7816)
Improved color balance for QImaging cameras (TT7749)
Improved icons in Charting module (TT7762)
Improved labelling of regions for multi-timepoint measurements. The region numbers now restart for each timepoint (TT7765)
Improved memory management in Classifiers – this allows us to classify larger images without running out of memory (TT7718, IS08596)
Improved performance of selections in Measurements vide (TT7987)
Improved quality of fast restoration (TT6679, TT7604)
Improved reading of position count from Ludl filter wheels (TT7529)
Improved responsiveness of QImaging camera controls (TT7659)
Improved speed of selecting measurements (TT7634)
Objectives are now labelled with their magnification rather than with a number (TT7768)
Open/close shutter key (F8) now toggles the shutter for the current lightpath rather than using the first fluo shutter (TT7927)
Removed the ability to zoom image sequences in “thumbnail” mode as it could be confusing (TT7770)
When a Z acquisition is finished, we now return to the starting Z position rather than leaving the drive at the top (TT7625)
When binning is changed, the camera exposure is now automatically adjusted to keep the image brightness the same (TT7629)
Worked around bug in Leica DMI6000 firmware that would report an incorrect Z step size (TT7810)
Worked around problem that could corrupt libraries if the library was on a server and was opened by a PC. This only affects certain types of server (TT7912, IS09045)
Mac: Fixed problem that could cause malformed 3D measurement feedback and crashes (TT7995, IS09195)
Mac: Fixed crash on quit if the Voxel Spy palette is visible (TT7687)
Mac: Fixed problem that could cause a crash if the wand tool was used on the video preview (TT7720)
Mac: Fixed problem that could cause the focus feedback to go beyond 100% (TT7734)
Mac: Fixed problem that could cause the HR Renderer to stall if channels were hidden (TT7740, IS08192)
Mac: Fixed problem where it was not possible to drag a Classifier to the bottom of the list in the palette (TT7974)
Mac: Fixed problem where only integers could be entered for ND filters – fractional values are now permitted (TT7801)
Mac: Fixed problem where video crop area could be lost if the view preview is hidden and then shown again (TT7790)
Mac: Ludl MAC5000 is now driven through USB instead of serial – this improves speed and reliability (TT7423)
Mac: Tidied some of the charting dialogs (TT7591)
Mac: Phylum is now a Mach-O executable. It uses a bundle that contains all the modules, so only a single “Phylum” application icon is visible. Modules can be managed through the Finder “Get Info” dialog (TT7650)
Windows: Color popup in light path dialog is now a rainbow rather than a range of contrasting colors (TT7631)
Windows: Fixed problem that could cause a crash when trying to edit a movie sequence in a read-only library (TT7731)
Windows: Fixed problem that could cause incorrect redraws when looking at a sequence in timeline view while acquiring (TT7633)
Windows: Fixed problem where “Maximum distance between objects” in the “Tracking” dialog would not be remembered when the dialog was next opened (TT7799, IS08628)
Windows: Fixed problem where it was sometimes not possible to drag tasks onto a movie sequence with a dual-monitor setup (TT7827)
Windows: Fixed problem where Measurements could crash when deleting tracks from a session (TT7630)
Windows: Fixed problem where palettes would reappear if any application is maximised after clicking the “show desktop” button in the task bar (TT7719)
Windows: Fixed problem where the name of a Classifier could become corrupted when you drag and drop them (TT7713)
Windows: Fixed problem where Phylum could appear to lock up if the Navigation forward/back icons were clicked very quickly (TT7958)
Windows: Fixed problem where Voxel Spy palette would not always work when first shown (TT7593)
Windows: Fixed problem with dragging ROIs in the XZ and YZ planes of the Image view (TT7698, IS08565)
Windows: Fixed problem with video controls that have negative values (e.g. offset control on C9100-11) (TT7874)
Windows: Improved performance of importing files (TT7923)
Windows: Improving handling of out-of-memory errors (TT7587)
Windows: Made selected state of buttons clearer (TT7627)
Version 3.1 (31 Jan 2005)
Added “Slice View”. This view provides an alternative way of visualising 3D images.
Added support for “Light Paths”. A light path is a combination of device and shutter settings for a particular channel. Light Paths can be switched during an experiment or manually from the “Video Preview” window. Light Paths replace the functionality previously provided by “States” (TT7268)
Added support for acquiring channels at different rates. This allows “reference” channels to be acquired more slowly, increasing overall performance.
Added support for ASI MZ2000 XYZ stage controller
Added support for Improvision Acquisition Hub (TT7533)
Added support for Leica DM4000/5000/6000 contrast modes (TT6626)
Added support for Ludl MAC5000 filter wheels
Added support for Nikon TE2000 and 90i microscopes (90i is Windows-only) (TT7574)
Fixed inconsistency with naming of “Experiment Log” on Mac and Windows (TT7395)
Fixed problem where 3D feedback of measured objects could be out by up to one voxel (TT7511)
Fixed problem where closing the library while an acquisition experiment is running would cause an endless loop of error messages (TT7567)
Fixed problem where opening a library or library clipping created on a different platform could cause a crash or incorrect behavior (TT7522, TT7571)
Fixed problem where the exposure time for the RTM would not be reported properly in the experiment log (TT7523)
Fixed problem where very long measurement session names would cause chart extraction to fail (TT7391)
Fixed problem with acquisition where shutters would not be opened for auto-exposure (TT7369)
Fixed problem with charting where clicking on the legend title of a pie chart would cause a slice of pie to be removed (TT7454)
Fixed problem with charting where extracting measurements that were all the same would cause the chart not to be drawn (TT7404)
Fixed problem with charting where pie charts did not display percentages correctly (TT7456)
Fixed problem with experiment logs where duplicate device change entries would be recorded (TT7443)
Fixed problem with making movies from the HR Rendering view where the view contains surface-rendered objects. In some timepoints, the objects would not be rendered (TT7466)
Fixed problem with Olympus microscope support where the positions of filter wheels 1, 2 and 3 were not displayed correctly (TT7439)
Fixed problem with Sutter DG-4 where brightness settings for each filter would not be saved and restored properly (TT7418)
Fixed problem with Zeiss microscope support where controlling the Z drive on older microscopes could cause an internal error (TT7390)
Improved error message when an incorrect License Server password is entered (TT7476)
Improved measurement of black reference for RTM (TT7479)
Improved naming of X and Y axis menu options in Charting when chart is in “Histogram” mode (TT7458)
Improved performance of experiment log – this in turn improves performance of image capture (TT7446)
Improved performance of sorting measurements if any measurements are selected (TT7498)
Improved reporting of problems when opening Metamorph STK files (TT7389)
Mac: Fixed crash if the “Open Read-Only Library” warning is cancelled (TT7505)
Mac: Fixed problem where opening a library created in Phylum 1.4.4 could cause Phylum 3.1 to crash (TT7556)
Mac: Fixed problem where removing data from the “Data” view of a chart could cause a crash (TT7467)
Mac: Fixed problem where the column headers would not be updated properly after dragging a selected measurement column to a new position (TT7504)
Mac: Fixed problem where the Phylum build number would not be reported properly in the session log (TT7530)
Mac: Fixed problem with Charting where changing the source of a pie chart from “Volume” to “Category” would not work properly (TT7460)
Mac: Fixed problem with Charting where hiding the “Y” axis of a histogram would not work properly (TT7462)
Mac: Fixed problem with Charting where pressing “enter” would not “OK” dialogs (TT7455)
Mac: Fixed problem that could cause error 1 when trying to modify an image that was an exact multiple of 4096 in size (TT7419)
Mac: Improved behavior of the image view when all channels are turned off (TT7431)
Phylum help files are now PDFs and are available from the “Help” menu (TT7457)
Replaced “frames per second” with “timepoints per second” in acquisition. This is a more accurate description (TT7394)
Windows: Added support for deleting chart data from the “data” view (TT7468)
Windows: Fixed hiliting of column headers in the measurements view – they now behave like buttons (TT7497)
Windows: Fixed problem where palettes could be restored off-screen if the screen resolution changes (TT7509)
Windows: Fixed problem where unchecking a device in the “Devices” preference panel would uncheck its child devices (TT7531)
Windows: Fixed problem with Navigation palette where channel controls would be rebuilt more often than necessary. This prevents flicker and other unwanted behavior (TT7541)
Windows: Fixed problems where “Cascade” and “Tile” menu items would not resize the “Session Log” window correctly (TT7502)
Windows: Fixed spelling of “Category” in Charting (TT7459)
Windows: Fixing problems with Voxel Spy palette showing text in the wrong position (TT7492)
Windows: Improved behavior of “magic wand” tool when clicking within existing ROIs (TT7434)
Windows: Worked around limitation of Intel Indeo Video 4.5 AVI codec where minimum image size if 640x480 pixels (TT7537)
Version 3.0.2
Added option to turn off “Automatically Join Broken Tracks” in tracking (TT7246)
Added support for Olympus IX81 and BX61 microscopes (TT7267, TT7276)
Added support for ORBIT 2 high-speed shutter (TT7258)
Added support for QImaging cameras (TT7310)
Added support for Sutter DG-4 (TT7261)
Fixed problem where measurements feedback could appear incorrectly in the HR Renderer if the resolution limit was not set to “highest” (TT7336)
Fixed problem where size thresholds would not always be honoured if “Separate Touching Objects” is used in a Classifier (TT7362)
Fixed problem where Phylum could crash when deleting measurements from a measurement session (TT7210, IS06719)
Fixed problem with reading some ICS/IDS files (TT7278, IS07029)
Fixed problems with palettes not minimising when Phylum is minimised and not undocking correctly under some circumstances (TT7373, TT7374)
Fixed memory leak in restoration (TT7264)
Improved behavior of Movie Sequencer. Brightness, density etc. are now set to initial values derived from the sequence (TT7340, IS07119)
Improved labelling of charts with mainly negative values (TT7206)
Improved memory management when making a movie using the HR Renderer and multi-timepoint sequences. This should help to avoid “out of memory” errors with large sequences (TT7173, IS06539)
Improved performance of Classifier “fill holes” option (TT7335)
Improved performance when working with large datasets by using memory-mapped files for image sequences (TT7120)
Mac: Fixed cosmetic defect in “Measure Objects” dialog “session name” field (TT7281)
Mac: Fixed problem where it was not possible to draw very short lines with the line tool when the image was zoomed in (TT7244)
Mac: Fixed problem where renaming a chart plot could cause an error (TT7322)
Mac: Fixed problem where some menu items were disabled when a chart is open (TT7321)
Mac: Fixed problem where track ID in image view only had space for 4 digits (TT7228)
Mac: Fixed problem with charting where changing axis units did not always work (TT7318)
Mac: Worked around bug in Mac OS X 10.2.8 on G5 machines which caused the Iterative Restoration module to give incorrect results (TT7204, IS06603)
Windows: Fixed inconsistency between “Renderer” menus between Mac and Windows (TT7269)
Windows: Fixed problem where artefacts could appear on the image window if the scale factor was not an integer (TT7311)
Windows: Fixed problem where selecting measurements in the measurements view could sometimes cause a “pure virtual function call” error (TT7259, IS06910)
Windows: Fixed problem where tools would not initially be selected in some views (TT7364)