06.11.12: Version 0.937 released

• Corrected the signal integration procedure: function aip.cpp replaced with aip2.cpp, the previous one returned an error on a very small fraction of pixels.
• Updated the display in MicrobeTracker to display cell width and the average values for a selected group of cells.
• Updated logvalley function to introduce minimum LoG value (logthresh parameter) and cross detection between LoG and Valley (crossthresh parameter).
• Updated cell division function to use the exact procedure instead of an approximated one.
• Minor updates in peakfinder, dispcellall, plothist, kymograph, spotFinderZ, joinspots, and intprofile functions.

05.01.12: Version 0.936 released

• Added two tutorials: Accessing internal variables and Extending MicrobeTracker.
• Added a description of cell outlining algorithms.
• Added access to globals in Text-based Batch Mode.
• Corrected a bug in the logvalley function, which used to fail in "none" regime.
• Corrected a small bug in the saving background-subtracted images so that when a single image is saved it does not necessarily get a number added at the end.
• When changind polarity of the cells, mesh orientation remains clockwise from now on.

04.10.12: Version 0.935 released

• Added interpolated outline regime in algorithm 1 (with interpoutline, interpSigma, interpWeights parameters).
• Changed the edge/valley detection routines (removed "edgevalley" and replaced it with "logvalley" and "edgeforce" functions).
• Added possibility to not split (and discard) cells near the boundary (with splitbndcells parameter).
• Fixed a bug in getting signal for algorithm 1, which used to occasionally lead to negative signal.
• Fixed a bug in joinspots, now there is a way to output data in microns rather than pixels.
• Fixed a bug in SpotFinderZ, now the figure does not shift or disappear for images larger than the screen.
• Fixed small bugs in MicrobeTracker and peakfinder which caused occasional program failures.
• Fixed a bugs which used to cause histogram-producing tools to display NaN for the mean value.

02.17.12: Version 0.934 released

• Fixed a bug in SpotFinderF.
• "mindist" parameter replaced with "mindistold" and "mindistnew" in peakfinder.
• Added a possibility to account for shift between fluorescence (signal) and phase contrast images (see Shift of fluoresence images relative to phase section).
• Improved signal addition routine in MicrobeTracker (improved performance and eliminated rare errors which used to happen for small cells).

11.30.11: Version 0.933 released

• Fixed a bug in cell shifting in MicrobeTracker, which used to make cells that split on the first frame in a timelapse to shift to the left top corner on frame 2.
• Improved cell selection on frame change method in MicrobeTracker and added the option (now default, parameter delchildrenonredetect to change) to delete all progeny of a cell on all future frames when doing selected cell detection in a timelapse.
• Now the image of a removed cell in manual joining is correctly removed.
• Functions dispspot, dispspotsall and dispspotsgrid renamed to dispcell, dispcellall and dispcellgrid, respectively and modified. Added cellmovie function.
• Corrected the sign of integrated signal calculation for flipped cells.
• Added an option to display signal profiles in peakfinder (for parameter adjustment).

09.09.11: Version 0.932 released

• Fixed bugs in SpotFinderF tool.
• Added a possibility in SpotFinderZ to perform detection in a range of frames.
• Added minor features and better documented SpotFinderZ, SpotFinderF, dispspotsall, and testspotprecision tools.
• Fixed a bug in plothist tool (used by most histogram-plotting tools) to allow adding modifiers when using multiple cell lists.
• When changing frames in MicrobeTracker, selected cells are not selected anymore in timelapse=0 regime based in the first cell.
• Fixed a bug in MicrobeTracker with splitting on frame 1 using algorithm 2.

07.14.11: Version 0.931 released

• Fixed a bug with signal calculation, which resulted in consistently lower signal (~1.4 fold) on 32-bit Windows systems. Please, recompute if these data are going to be used in comparison with the ones obtained on 64-bit systems (which always worked correctly). This change was introduced in the latest variant of version 0.930.
• Added control parameter ("Shift limit") for "sticking" to pixel centers in SpotFinderZ (trade-off between precision and ocassional misfitting). Added a test function testspotprecision to identify if this parameter needs to be adjusted.
• Minor inprovements in the Text-based Batch Mode (saving/loading, adding comments, help).
• Minor correction in cell numbering after manual splitting.

06.08.11: Version 0.930 released

• Fixed minor bugs in manual refining, inverted image background subtraction, cell addition on empty frames, manual splitting in timelapses, export mode.
• Fixed minor bugs in saveimagestack tool.
• Added missing alg1.set parameters file.
• Added joinspots tool to the suite.
• Updated histogram-plotting tools (such as lengthhist, inthist, etc.) to suppress figure output if necessary. Fixed minor bugs in these tools.
• Added support for field names other than 'spots' to dispspots / dispspotsall / dispspotsgrid.

03.23.11: Version 0.929 released: expanded input-output options of the suite

• Added native (without BioFormats) reliable support for TIFF stacks into the relevant suite components.
• Added tools for saving and loading image stacks (loadimagestack and saveimagestack).
• Added tools for outputting some data into Excel format (exportcells2xls and exportspots2xls).

03.16.11: The paper describing the suite appeared on the journal's website (PubMed, journal).

03.08.11: Version 0.928 released

• Fixed a bug in the recently added signal integration function that caused program crashes.
• Minor changes in accessory functions.

02.07.11: Version 0.927 released

• The previously neglected Text-based Batch Mode improved and documented.
• A bug in backgroung subtraction for inverted images corrected.

02.04.11: The suite has been deposited to SourceForge website via SVN for further development.

01.26.11: Version 0.926 released

• Enhanced the possibilities of Manual Operations. Added splitting cells on click and added support for Time-lapses, where manual operations now update the lineage information.
• Changed the signal intergation routine. The new routine is 2x slower but exact when integrating the signal in pixels only partially intersecting the segment of the mesh. The previous version was using an approximation. The new version is C-based and currenty only compiled for Windows, on other platforms the old one will be used meanwhile.