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ChangeLog

LineageTracker Changelog

v1.2.4 (11th August 2013)

It is possible to add both daughter cells at the same time by highlighting the parent cell, moving to the next frame and highlighting the two daughters, then clicking on 'Modify Daughters'.
Fixed bugs caused by image listener behaviour apparently changing slightly between version 1.46 and 1.48 of ImageJ.

v1.2.3 (27th March 2013)

Software identical to v1.2.2 but now released under the Apache v2.0 Licence.

v1.2.2 (20th March 2013)

Highlight all cells option can now rewind back to the start of each track if a cell in the middle of an experiment is clicked.
Fixed a bug in tracking which causes a memory error if the frames at the end of an experiment contain no cells.
Any action caused by clicking a button causes the buttons to 'grey out' until the action has completed, to make it obvious that something is happening.
Tracking files no longer have the experiment name as prefix (this can be changed by selecting 'old file format' in Preferences).

v1.2.1 (24th January 2013)

Fixed a bug where plugins won't load if the filename is in lower case.

v1.2.0 (4th January 2013)

Experiment loader now recognises compressed images (Creating and segmenting new experiments takes roughly twice as long with compressed images but data takes up half as much disk space).
Use call("ij.Prefs.set","TrackApp.CompressedImages",true) to allow new experiments to use compressed images.
Segmentation now records X & Y co-ordinates separately from the bounding box and sub-pixel resolutions are now recorded correctly. This improves some cell motility measurements.
New file format for cell data, which will allow for more than 8 colour channels. Old format data files are still saved for backward compatibility.
The plugin window is now scrollable when there are a lot of plugins installed.
The select experiment window resizes better to show more experiments.

v1.1.6 (10th October 2012)

Fixed bug where creating a new experiment in a macro always creats it in the last used root directory instead of the directory provided by the macro.
Removed old and obsolete methods from the tracking and cell division code. Highlight All Cells now draws tracks if 'overlay tracks' is ticked.
It is now possible to pass parameters to some plugins when calling from a macro.
Edit Preferences plugin is now included in the main LineageTracker distribution
Load Experiment window can filter experiment based on whether they have image data or not. Remembers last values of Confirm Changes and Overlay Tracking. Clicking 'Cancel' when running tracking from the viewer will abort the tracking (instead of using the old settings). This is more like the expected behaviour.
Saves cell centres in addition to bounding box so that cell positions are recorded more accurately.

v1.1.5 (4th September 2012)

When called from a macro, can work without loading images to speed up batch operations. Support for compressed files added which stores masks as PNG and image files as compressed TIFFs. Go To Cell now correctly zooms in to the chosen cell.

v1.1.4 (27th April 2012)

Improved support for calling 'Create Experiment', 'Segmentation' and 'Experiment Viewer' from the ImageJ macro language to improve automation. Memory usage has been decreased. Channel colours can be selected in the 'Edit Channels' dialog box.

v1.1.3 (2nd February 2012)

Removed some unused code which was leftover from earlier versions.
Fixed bug which caused a crash if a plugin required a jar which was missing.
New tracking method with simple nearest cell division detection added.

v1.1.2 (20th September 2011)

Further improvements to memory handling. Most memory is now released back to ImageJ when the image windows are closed.
Segmentation preview now displays up to 3 channels.

v1.1.1 (unreleased, test version)

Improved memory handling, first steps towards fixing memory leak.

v1.1.0 (12thSeptember 2011)

Breaks compatibility with old segmentation plugins - editSettings returns a boolean which specifies whether OK or CANCEL was clicked so extending classes can ignore the returned values.
Analysis plugins also appear in a pop-up window which allows them to be activated once then deactivated, which is faster than having to use the selector to unselect them to return to 'normal' behaviour.
Segmentation editor can show channel colours in edit channels window. If an image has an associated LUT, these get chosen for the channel colours.
Saves the mask colour in the experiment data.
Plugins are now listed in alphabetical order instead of the arbitrary order they were displayed in in earlier versions.
If a preview window is open and segmentation settings are changed, the preview is re-drawn.

v1.0.7 (17th August 2011)

Included new redrawOverlay() method in Image5DWithOverlay to get around the problem where overlay isn't automatically updated after a 'Clear Overlay'.
Fixed bug which crashed the viewer if 'Cancel' was clicked when retracking cells.
When the mouse is clicked to select/interact with a cell, if an analysis plugin is called, don't leave the ROI on screen automatically.
Exporting lineage intensity to a results table: Each daughter cell can now include the intensity of the parent cells, which may be useful for some data analysis. Data interpolation method updated to handle these cases.
Segmentation can be cancelled without quitting the application.
'Merge Cells' plugin for the Viewer is bundled with the application.

v1.0.6 (20th July 2011)

In previous versions, closing other image windows can sometimes break the connection between the cell window and the 'control box' windows. This appears to be fixed.
Debug levels can be stored in the ImageJ Prefs file so it can be turned on or off without recompiling. Use call("ij.Prefs.set","TrackApp.DEBUG","true"); to turn debugging on.
Fixed bug in tracking where the division detection algorithm expected two image channels, even when division detection was disabled (this was left over from when the software was developed to handle 2 channels only).

v1.0.5 (18th July 2011)

Delete will remove multiple cells if an area ROI is drawn on the image.
Drawn ROIs are retained when frame is changed but cell outline ROIs (which are shown when a cell is selected) are removed. This speeds up cell and lineage editing.
After saving data, the view returns to the current frame instead of jumping to the end of the experiment.
Allows interpolation of exported intensities where there are gaps in tracking.
Mask channel visibility is now retained when the experiment is resaved.
Fixed bug where clicking 'Cancel' when choosing data directory gave a blank (null) directory.
Fixed bug where multi-channel z-stacks only import a single frame. Side effect is versions of ImageJ prior to 1.45n may throw up an additional dialog box which will need clicking.
Allows multiple cells to be deleted by drawing an ROI and clicking Delete.
Main LineageTracker jar file can now be renamed as anything and plugins contained within will still be located. Extra plugins still need to be within a jar file with 'Tracker' in the name (to speed up locating plugins).

v1.0.4 (5th July 2011)

'Create From Open' detects multiple colour channels and offers to split.
Double-click now works in selecting from list of experiments.
Fixed bug where if all ROIs are deleted in a frame, the ROI file is left on disk so the nonexistant ROIs are reloaded next time.
Added java interfaces to allow analysis plugins to easily add/remove cells and rebuild the outlines - future plugins will be able to use these to edit the cell data.

v1.0.3 (22nd June 2011)

[Internal distribution only, not publicly released]
Can output mean intensities not just integrated.
Fixed bug which saves tracked data as 'null.tracked'
Doesn't output fluorescence info for un-measured channels.
'Frames' now available as a frame interval name instead of just time-intervals.

v1.0.2 (1st June 2011)

Draws arrows connecting dividing cells when drawing lineages.
If compiled in 'debug' mode, can highlight all cells in a frame.
Experimental: drag and drop support for text files holding cell positions (requires extra libraries, to be made available later).
More errors and exceptions are caught by the software so macro execution isn't interrupted.
Only load in the first 'n' frames if info.xml is changed to hold a smaller number of frames than exists in the stacks.
Plugins can be within jar files to make distribution easier.
New dialog box for choosing or creating an experiment.
Different tracking methods are possible in the segmentation application.

v1.0.1 (28th March 2011)

Interfaces for plugins re-written.
Support for multi-channel experiments.
Faster handling of ROIs and drawing mask channel.
Adjustable frame interval for segmentation preview.

version 1.0.0

[Internal distribution only, not publicly released]

Known Issues

Under certain circumstances using ImageJ, the LineageTracker plugin displays a 'java.lang.UnsatisfiedLinkError' and stops loading. This is caused by an incorrectly installed QuickTime Java plugin. Calling LineageTracker for a second time makes it load as normal. This error does not occur when using Fiji.

There is a problem with running tracking after manually editing cells. If the data has not been saved to disk, the edited cells sometimes disappear.

Future Changes

Sort out problem where user drags a cell outline ROI away from the cell. The new ROI position is sometimes saved where the user dropped it.

Change the method of selecting and calling analysis plugins to make it easier to turn them on or off.