See ChangeLog or "svn log" for details of evolution. Version history: -------------------- v1_3b: Cengiz Gunay, 2012/09/24. Public beta release. - More stable support for reading ABF and reading/writing Neuron binary and text files. - Lots of new utility functions. - Many bugfixes thanks to new users (e.g., Vladislav Sekulic, Anca Doloc-Mihu), so more options and stable operation for recordings from different organisms and systems. - Took Readgenbin out as an independent tool (see it on github). - Support for voltage and current-clamp data as paired traces and related tools. VC data is used for Hodgkin-Huxley type channel data fitting. - Better unit support for data fitting and plots. - Better handling of NaNs in database operations. - New data measurements like "time to 1st spike". - Improved KL divergence calculation. - Optimized DB indexing and addressing operations, sped up 50x. - uniqueValues now preserves row order. - Improved use of NNet and SVM classifiers v1_2b: Cengiz Gunay, 2008/10/31. Public beta "Halloween" release with bugfixes and support for NeuroShare-compatible files. - NeuroShare support to load many acquisition formats in Windows (see http://neuroshare.org). Included DLLs and utility functions. - Regular expression support in querying and indexing databases. - Added convenience 'group by' functionality similar to that of SQL's - Added citation reminder in license document - Included missing files for the filtering-based spike finder - Plot improvements: - histogram bar plots - Blank plot objet are properly handled. - Workaround for compatibility with compiz-fusion. - Made CGMPLOT an optionally separate package (see website). - New stacked 3D image plot. - Proper handling of line colors in superposed plots. - Joins better handle NaNs and accept multiple pages. - Defaults changed for balancing classifier input probabilities. - website update, created example files for Neuroinformatics manuscript - Major bugfix to invarValues for asymmetric databases. - Improved HDF5 handling by Li Su and CG. Several changes and additions. - Can now merge old (PCDX) and new (HDF5) recorded bundles v1_1b: Cengiz Gunay, 2008/02/11. Public beta bugfix and feature release. Warning: old physiol_cip_traceset_fileset objects will be incompatible and will have to be re-created. - Added SQL import/export functions using Matlab Database Toolbox. - improved HDF5 acquisition data and metadata import with ns_load_traces. - simplified database + dataset bundle generation from raw physiology data. - Tom Sangrey added customized Butterworth filters for traces sampled at rates other than 10KHz. - Li Su provided bugfix to his improved findspikes routine. - Added examples to manual. - Added missing functions such as gettracelist2 - improved plotting: - Improved chan_db plots. - Improved doc_plot, can reference using labels now. - histogram plots can normalize. - plot_stack can now find maximal ranges. - can display database values with boxplots. - Other miscellaneous plot enhancements. - Major bugfix for NaNs in compareRows, joinRows, princomp, and plotScatter - added several new overloaded operators to tests_db, such as unique, sqrt, uminus - Documentation update. - can make a database from matlab structure. - added spike width calculation at a fixed voltage. - changed the way joinRows uses parameters. - added tests_db/approxMappingNNet function that uses the Neural Network Toolbox. - added option to balance input probabilities of classes to map. v1_0b: Cengiz Gunay, 2007/10/10. First public beta release - moved to subversion control from CVS - organized files into subdirectories - included all additional utilities - made a installable package available for download - added a Academic Free License and copyright statement - supports NeuroSAGE HDF5 input files for recorded physiology data - can load from subdirectories in params_tests_fileset - misc improvements of plotting functions (margins, titles, etc.) - added examples into manual - allow using covariance matrix for calculating Mahalonobis distance in ranking - new function to find a ll best matching neurons - support inset plots at arbitrary axis locations - extend querying to allow columns and pages. also better optimized. - added support for plotting channel variables - improved cluster job submission v0_10b: Cengiz Gunay, 2007/03/22. Beta version. - automated function reference generation from Matlab source for PDF and HTML manuals - revamped plot generation by making plot_abstract solely responsible for frame - superposition of stacked plots now possible - several improvements to plotting - added algebraic operations to tests_db including transposition - improved comparative analysis of 3D DBs - started using arrays rather than cell arrays during analysis to simplify calls - new layouts for plotting neurons, flexible selection of traces to display - misc new database operations, such as enumerating unique values - improved firing frequency plot - generic 2D image plots - added parameter to load parameter files with different trial numbers - added a utils/ directory for external programs - added support for loading binary Neuron files, compressed Genesis files. v0_9b: Cengiz Gunay, 2006/02/15. Beta version. - Improved plotting in many ways including with self-resizing plots. - Vectorized many functions to operate on multiple inputs. - Improved spike shape measurements based on results from new morphologies. - Optimized for memory usage in merging, joining and ranking databases. - Compatibility issues with Matlab R14.3 fixed. - Added the concept of a bundle of a dataset and DB. - Allow comments in physiol cell files by Tom Sangrey. - Moved props out of spike_shape, into base class trace. - Added automated document generators that can hold plots or tables, etc. - Organized and automated how ranking documents are generated and added more plots. - Added specialized plot that can do f-I curves and similar plots. - Added script_array and subclasses to do automated analysis on the cluster. - Added .genflac support. - Allow adding files to existing filesets and loading DBs of added files only. - Added presets for comparing a limited set of measures and specify weighting. - Allow modifying DB contents with paren addressing rows and columns. v0_8b: Cengiz Gunay, 2005/10/19. Beta version that has improved analysis and plotting functionality, and documentation. Database object format has changed, which makes this revision binary incompatible with earlier created DB and dataset objects. v0_7b: Cengiz Gunay, 2005/05/04. Beta version that analyzes each spike individually and uses improved threshold finding method. v0_6b: Cengiz Gunay & Jeremy Edgerton, 2005/03/14. Beta version that can load physiology filesets with pharmacology data. v0_5b: Cengiz Gunay, 2005/01/25. Beta version that can work with PCDX files. v0_4b: Cengiz Gunay, 2005/01/11. Beta version with pulse spike characteristics and database matching tools. v0_2b: Cengiz Gunay, 2004/09/16. Beta version of fileset and db classes. v0_1b: Cengiz Gunay, Aug, 2004. Beta version of base classes trace, spikes, spike_shape, period, and cip_trace.