---

NLMorphologyConverter 

• Plan for first major stable release: Version 1.0.0
  
• Activate scripting support for publicly available versions (Lua at least, and probably Python also - both are already tested and working in general, but need a little more polish to complete the support to a releasable standard). Allows internal neuron data structures to be constructed, navigated and queried, thereby enabling user-extension of the converter functionality. (Example scripts will be provided - e.g. custom neuron importer, custom neuron generator, custom file format exporter, custom statistics generator.)
• Provide C++ SDK, python wrapper..
  
• Add general support for non-soma contours (can already force import by using hint options).
  
• Possibly add support for preserving more data between Neurolucida formats (i.e; data which this software doesn't particularly care about, but might be useful for users...)
• Fix any unnecessary limitations and outstanding bugs in current functionality.
• Testing regime: full support for 1D formats (will only test branch lengths/diameters)
• Generally improved documentation.
  

• Call for feature requests - the main converter functionality is unlikely to change significantly once version 1.0.0 is reached. Please email any additional bug reports or feature requests to  feedback AT neuronland dot org
  

Version History

• 0.10.0.dev - 10th January 2016  (NOTE: * incidates in-progress or broken feature: don't expect it to work well, if at all. Other features should be quite stable.)
  
• Windows release.  Extra release between 0.9.0 and version 1.0.0 (which is very heavily delayed due to an unfortunate lack of development time).  This is a major release, with several new file formats now supported, many bugs fixed, and several new features added.
  
• Installation: Windows: NLMorphologyConverter executable location now automatically added to system PATH.
• Improvement: case insensitive output format name check.
  
• Improvement: case insensitive style name check.
  
• File format Aramal support added (Import and Export. This is an old format, and similar in many ways to SWC. Support is added due to appearance of 4 files in NeuroMorpho:jaffe archive.)
• File format Bannister support added (Import only. This is a 1D format (only contains length + diameter). Support is added due to appearance of 6 files in NeuroMorpho:larkman archive. See also --set1Dxxxxxx options for configuring artificial branching pattern.).
  
• File format ImarisHDF import support added
  
• Note: no export added. 
  
• Imports Filament data. 
  
• Experimental, much more test data needed. Please send! 
  
• Note: There is currently no Imaris data in NeuroMorpho database.
  
• Note: there is a known issue with looping filament data preventing successful import.
  
• File format Korogod support added (Import and Export. Experimental. found in ModelDB, Korogod et al 1999. ).
• File format NeurolucidaDATClassic support added (Import and Export. seen in NeuroMorpho:mailly and NeuroMorpho:bausch archives.)
• File format renamed:  LNeuronAmiraMesh format renamed to AmiraMesh.  Export LNeuron style with --style lneuron.
• File format renamed:  MorphML format renamed to NeuroML (MorphML will still work if specified as output format, however..)
• File format renamed:  NeurolucidaClassic renamed to NeurolucidaASCClassic (for consistency with addition of legacy NeurolucidaDATClassic binary format)
  
• General information preservation:
• Preservation of dendrite type (unspecified (basal), apical)
  
• Neurolucida information preservation:
  
• preservation of terminal types between NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML
• *preservation of colours between NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML
• Spine support:
  
• *added support for spine contours (e.g. as obtained from ImarisHDF format).
• see also --spinesToBranches command line option.
  
• *Fix for AmiraMesh import (AmiraMesh ASCII 1.0 files: no longer assume sample point diameter data is included. More general treatment of data fields order.)
  
• *Fix for AmiraMesh import (general support for SkeletonGraph type)
  
• *Fix for AmiraMesh import (general support for HxSpatialGraph type)
• *Fix for AmiraMesh export (add support for multiple styles:  'lneuron', 'skeletongraph', 'spatialgraph')
• Fix for Eutectics import (better file validation, ignore empty lines anywhere in file.)
  
• Fix for Eutectics import (better file validation, allow files which are missing certain expected header text: permits 4 files from NeuroMorpho:Fyffe archive. See also --strictValidation option)
• *Fix for NeuronHOC import (various bug fixes, new HOC parser)
• Fix for NeuroML import (recognize <neuroml> as a root xml tag, as well as <morphml>).
• Fix for NeuroML import/export (some tweaks to experimental version 2.0 support. Missing support for spines, markers. Not fully tested, not recommended for general usage...)
• Fix for NeurolucidaASC import/export (support for distinguishing apical dendrites)
• Fix for NeurolucidaASC import (better file validation)
• Fix for NeurolucidaASC import (now aware of TreeOrder keyword)
• Fix for NeurolucidaASC import (now aware of GUID keyword)
• Fix for NeurolucidaASC import (now aware of MBFObjectType keyword)
• Fix for NeurolucidaASC export (support for neurolucida terminal types)
• Fix for NeurolucidaASCClassic import (ignore unknown Major id, rather than indicating failure...algorithm will usually be able to cope)
• Fix for NeurolucidaASCClassic import (fix for error being signalled for empty lines at end of file)
• Fix for NeurolucidaASCClassic import (fix for crash when markers are at end of file)
• Fix for NeurolucidaASCClassic import/export (support for distinguishing apical dendrites)
• Fix for NeurolucidaXML import (support difference between version 4.0 and 3.0, namely sub-trees tagged as "branch" in v. 4.0, vs. "tree" in v. 3.0)
• Fix for NeurolucidaXML import/export (support for distinguishing apical dendrites)
• Fix for NeurolucidaXML export (support for neurolucida terminal types)
• Fix for NeurolucidaXML export (support for neurolucida terminal types)
• Fix for NeurolucidaDAT import (safely ignore small section of 'corrupt' (?) data which can appear after DDCCBBAA terminal. Appears in NRX files in NeuroMorpho:buzsaki archive).
• Fix for NeurolucidaDAT import (cope with alternative sub-tree element tag 0x0209 - probably equivalent to NeurolucidaXML v. 4.0 usage of "branch" instead of "tree" to represent sub-trees.)
  
• Fix for NeurolucidaDAT import/export (support for distinguishing apical dendrites)
• Fix for NeurolucidaDAT export (support for neurolucida terminal types)
• Fix for SWC import/export (support for distinguishing apical dendrites)
• Fix for SWC import (support for unordered data, e.g. output from Neuromantic, where parent nodes may appear file after child nodes in the SWC file.)
• Command line options
  
• --style

• MorphML (style option allows user to choose the root tag)
  
• 'morphml' (default)
  
• 'neuroml'
• AmiraMesh
• 'lneuron' (HxLineSet)

• *'skeletongraph'
• *'spatialgraph'
• --spinesToBranches  (tree spines are coverted into small dendritic branches; global spines have no associated branch and so cannot be converted.)
• --test <file> <format> <logfile>  (run test regime on file, which is known to be in specified format. Outputs results to specified file. Overides any other options.  Please use this option to test any files which are causing problems, and send original file + test logfile.)
• --strictValidation (by default we relax the file validation conditions slightly, to allow certain files (which do not quite conform to the expected file format) from certain archives, to pass. This options requires files to strictly conform to file format specification.)
• Currently affects -
  
• Eutectics:
  
• Helper options for import of 1D formats (which contain only length-diameter information, so require that we invent branching angles for the 3D representation.)
  
• --set1DBifurAngle <angle>  (angle is in degrees. General. Binary child branches will split at this angle. Non-binary branch points will share this angle range. default 36)
• --set1DBifurAngleApical <angle>  (angle is in degrees.  overrides General setting. Defaults to General setting)
• --set1DBifurAngleAxon <angle>  (angle is in degrees.  overrides General setting. Defaults to General setting)
• --set1DRootAngleRange <angle> <range>  (angle, range are in degrees.  Range around angle which the dendrites root points will be spread. Default 90, 150)
• --set1DRootAngleRangeApical <angle> <range> (angle, range are in degrees. Range around angle which apical dendrites root points will be spread. Default 270, 45)
• --set1DRootAngleRangeAxon <angle> <range> (angle, range are in degrees. Range around 180' which the axon root points will be spread. Default 180, 45)
• --set1DBranchingPattern <pattern> (pattern can currently only be planar. More to come in the future.)
• Testing regime:
  
• updated to data in NeuroMorpho version 6.0. 
  
• NLMorphologyConverter is now capable of importing almost all file formats currently found in the NeuroMorpho archive.
  
• *various issues to resolve before entire archive passes the current testing regime.. (mostly Neuron HOC issues)
  
• including 5 damaged/incorrect files (3x NeurolucidaASC, 2x SWC), which have been manually fixed
• including various yuste archive ASC files which have manually fixed
  
• excluding 6 Bannister format files in Larkman archive (1D format, no export provided. Import is double-checked manually.).
  
• excluding various Neuron HOC files pending fixes for importer.
• + more
• private database: added supplied AmiraMesh 2.0, ImarisHDF ims, and NeurolucidaXML files.
• Note that NLMorphologyViewer has been updated (version 0.4.0) with all the fixes listed here, and can now display spine contour data (as found in ImarisHDF format..)

• 0.9.0 - 17th October 2010
  
• Windows release.  This is a major release, with many bug fixes, changes, and other improvements.  This is the final non-bugfix release before the first offical stable release (version 1.0.0).
• NeurolucidaXML format import/export support added (format is documented here -> https://support.mbfbioscience.com/index.php?action=kb&article=37).
• PSICS xml morphology format import/export support added (format is documented here -> http://www.psics.org/formats/morphology.html.)
  
• Generally improved error handling.
• Additional import/modify/export logging.
  
• General improvement of soma support accross all relevant formats (largely due to inclusion of soma data in testing regime).
  
• General improvement of marker point support accross all relevant formats (largely due to inclusion of marker data in testing regime). (Note that marker points are classed as global (not explicitly associated with specific substructure) , or explicitly associated with specific neuron structure - soma, or tree (i.e. axon or dendrite) branches.).
• Explicit spine data import/export support for MorphML, NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML, and NeuroZoom formats. Support spines as much as possible in Eutectics import. Spines are either global, or explicitly associated with tree samples).
  
• NeuronGeneric format renamed to NeuronHOC. Significantly improved NeuronHOC import and export algorithms. ***PARTLY DISABLED PENDING SOME FIXES - will be available in version 0.9.1 *** NOTE:  (UPDATE: delayed, and will be available in version 1.0.0.)
  
• ***DISABLED PENDING SOME FIXES*** Complete rewrite of importer. (Essentially now compiles and executes a subset of the HOC language - should be able to cope with: create, access, connect, pt3dclear, pt3dadd, for, proc, +more , while safely ignoring commands unrelated to tree geometry construction.)
  
• ***DISABLED PENDING SOME FIXES*** Many different commonly used HOC styles may be exported  (see --style option)
  
• ***DISABLED PENDING SOME FIXES*** Can import all HOC style which can be exported, and various slight variations of these styles which can be found in e.g. ModelDB.
  
• Can import NeuronSWC2HOC and NeuronNTSCable formats
  
• Remove explicit NeuronSWC2HOC format - now supported via NeuronHOC format (auto-detected by importer, and exported with --style swc2hoc)
  
• Remove explicit NeuronNTSCable format - now supported via NeuronHOC format (auto-detected by importer, and exported with --style ntscable)
  
• Fix for Douglas3D export (multiple soma contours will now be exported).
• Fix for Eutectics import (treat BTO and TTO points in the same way as MTO.).
  
• Fix for Eutectics import (allow OS,OCP,OE,DS,DCP,DE tags to be treated as soma contours. This is not default behaviour. See import option  --hintAllContoursAsSoma.).
  
• Fix for Eutectics export (soma: export all points, not just contour ends point!).
  
• Fix for Eutectics export (support for soma, axon, dend, structure name prefix customisation. Defaults are "cell", "ax", "d".).
  
• Fix for Genesis export (reactivated, fixed, and tested).
• Fix for Genesis export (support for soma, axon, dend, structure name prefix customisation. Defaults are "soma", "a", "d".).
  
• Fix for Glasgow import (marker data fixes).
• Fix for MorphML import (handle all the minor variations between different morphML versions - any version from 1.0 to 1.8.2, and should also work with the anticipated changes for version 2.0. See also command line export option --versionNumber).
• Fix for MorphML import (correctly handle all supported SI length units, i.e. meter, millimeter, micometer + older "..re" variations).
• Fix for MorphML import (algorithm now copes properly with arbitrarily ordered cable/segment data).
• Fix for MorphML import (cellBody/cell_body data, spine and freePoint/free_point data is now imported).
• Fix for MorphML export (cellBody/cell_body, spine, and freePoint/free_point data is now exported).
• Fix for MorphML export (support for structure name customisation).
  
• Fix for NeurolucidaASC import (general rewrite to simplify and optimize algorithm, and avoid problems which could potentially occur with unknown keywords).
• Fix for NeurolucidaASC import (correctly differentiate open and closed contours).
• Fix for NeurolucidaASC import (by default, contours with the (CellBody) property, or contours which have "CellBody", "Cell Body", or "Soma" as a substring are treated as soma contours. See also command line import option --hintSoma).
• Fix for NeurolucidaASC import (global and contour markers correctly distinguished.).
• Fix for NeurolucidaASC import (spine support).
• Fix for NeurolucidaASC export (update default format to be consistent with recent versions of Neurolucida. Older styles can be selected using the --style option).
  
• Fix for NeurolucidaASC export (marker names preserved).
  
• Fix for NeurolucidaASC export (various minor comment layout adjustments for consistency with files generated by Neurolucida).
  
• Fix for NeurolucidaASC export (spine support).
  
• Fix for NeurolucidaASC export (support colour customisation).
• Fix for NeurolucidaASC export (support for soma contour name customisation).
  
• Fix for NeurolucidaASC export (remove an artificial limit on the level of tree data indentation).
• Fix for NeurolucidaClassic import (where relevant, assign marker data to associated contour/branch, rather than considering all marker data as global).
  
• Fix for NeurolucidaClassic export (set header data correctly - file is original filename of imported file; min & max extents are calculated. Remaining data is set to reasonable defaults, generally 0).
• Fix for NeurolucidaClassic export (write all soma contours, instead of just the first).
  
• Fix for NeurolucidaClassic export (write marker data).
  
• Fix for NeurolucidaDAT import (support spine data).
  
• Fix for NeurolucidaDAT import (check for (CellBody) property - always treat as Soma data, whatever the contour name might be).
  
• Fix for NeurolucidaDAT export (support marker data - global, contour, and branch; support spine data).
  
• Fix for NeurolucidaDAT export (support colour customisation).
• Fix for NeurolucidaDAT export (always add (CellBody) property to soma contours).
• Fix for NeurolucidaDAT export (support for soma contour name customisation).
  
• Fix for NeuroZoom import (support spine data - note that spines are global, i.e. not associated with specific tree branches).
• Fix for NeuroZoom import (branch connection bug for non-binary trees in 'shortpath' layout style.).
• Fix for NeuroZoom export (remove some unnecessary junk).
• Fix for NeuroZoom export (first marker point per branch was not exported).
• Fix for NeuroZoom export (support spine data - all spines are global).
• Fix for NeuroZoom export (support colour customisation).
• Fix for NeuroZoom export (support for structure name customisation).
• Fix for Oxford export (reduce precision for sample data which otherwise occupies more than 8 characters).
  
• Command line options:
• Changes to existing options
• --omitMarkers removed and replaced with --omitAllMarkers, --omitGlobalMarkers etc...
• --omitSoma removed and replaced with --omitAllSomas, --omitSomas ...
  
• --warnings  various fixes for specific warning checks.
• --statistics  more statistics added
  
• New format-specific import hint options added (note: the need for hints often - but not always - indicates a lack of unambigious specification of key neuron structure in the format design which cannot be compensated for in other ways by the import algorithm.)
  
• --hintSWCStyle <style>. Helps the SWC importer to correctly import non-standardised SWC data files (ignored if not actually importing SWC data. Import will fail, if SWC data is not of the expected style)
  
• 'stdswc' (default)
  
• 'cnicswc'
• 'gulyasswc'
• --hintNeuronHOCEntryProc <proc_name>  (Identify a procedure of the HOC script, which encompasses the neuron geometry generation.  Several defaults: topol(), ???, to cope with all known styles.)
  
• --hintSoma <substring>   (Affects:  MorphML, NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML, NeuronHOC, NeuroZoom, PSICS)
• MorphML:    (Identify cable group name of segments which should be treated as soma segments. Default: "soma".)
• Neurolucida:  (Identify substring of contour names should be treated as soma data. This is in addition to "Soma", "CellBody" and "Cell Body".  We include this option because in many cases soma data is not tagged with the (CellBody) property.)
• NeuroZoom: (Identify substring of structure which should be treated as soma data. Default: "soma".)
• PSICS:         (Identify label of points/branches which should be treated as soma segments. Default: "soma".)
• --hintAxon <substring>   (Affects:  Eutectics, MorphML, NeuronHOC, NeuroZoom, PSICS)
• Eutectics:       (Identify substring of tree contours which should be treated as axon data. Default: "ax").
• MorphML:    (Identify cable group name of segments which should be treated as axon segments. Default: "axon".)
• NeuroZoom:  (Identify substring of structure which should be treated as soma data. Default: "axon".)
• PSICS:         (Identify label of points/branches which should be treated as axon segments. Default: "axon".)
• --hintDend <substring>   (Affects:  Eutectics, MorphML, NeuronHOC, NeuroZoom, PSICS)
• Eutectics:       (Identify substring of tree contours which should be treated as dendrite data. Otherwise all non-axon non-soma contours will be treated as dendrites.).
• MorphML:    (Identify cable group name of segments which should be treated as dendrite segments. Default: "dend".)
• NeuroZoom:  (Identify substring of structure which should be treated as dendrite data. Default: "dend".)
• PSICS:          (Identify label of points/branches which should be treated as dendrite segments. Default: "dend".)
• --hintAllContoursAsSoma  (Affects:  NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML, NeuroZoom)
• Eutectics:                (All non-dend, non-ax, contours are treated as soma data. Convenient for forcing all data to be imported. This data can later be modified with modify options.)
• NeurolucidaXXX:   (All contours are treated as soma data. Convenient for forcing all data to be imported. This data can later be modified with modify options.)
• NeuroZoom:           (All contours are treated as soma data. Convenient for forcing all data to be imported. This data can later be modified with modify options.)
• New modify options
  
• --reverseAllTrees.  (All branch points have child branch order reversed. - this has no physical affect on the tree, and only affects branch ordering in the file format.)
• --reverseTrees a,b,c.  (Specified trees have child branch order reversed.)
  
• --omitSomas <comma_delimited_list_of_soma_ids>
• --markersToSpines [all | <"marker name">]  (will automatically convert markers which match the specified substring to spines.).  Only relevent for formats which have named markers.
  
• --spinesToMarkers <"marker name">  (will automatically convert spines to markers with the specified name).
  
• --mapGlobalSpinesToBranches <limit>  where limit is max possible distance from branch sample (um).  (map global spine data  (i.e. spine data which isnt explicitly associated with a specific branch)  to specific branches - affects NeuroZoom and MorphML formats at the moment).
• --mapGlobalMarkersToBranches <limit>  where limit is max possible distance from branch sample.  (map global marker data  (i.e. marker data which isnt explicitly associated with a specific branch)  to specific branches - affects NeuroZoom and MorphML formats at the moment).
• --forceMarkersGlobal  Markers which are associated with soma or tree structure, are detached and made global.
  
• --forceSpinesGlobal  Spines which are associated with dendrite structure, are detached and made global. (automatic for NeuroZoom...)
  
• --renameMarkers <oldname> <newname>    Change the name of a marker.
  
• --omitAllMarkers.  (Omits all markers, whether global or associated with specific soma or tree structure. Only relevent when exporting to file formats which support marker data.)
• --omitGlobalMarkers.  (Omits global markers, i.e. those which are not associated with specific soma or tree structure. Only relevent when exporting to file formats which support global marker data.)
• --omitSomaMarkers.  (Omits markers which are associated with soma structure. Only relevent when exporting to file formats which support marker data.)
• --omitAxonMarkers.  (Omits markers which are associated with axon structure. Only relevent when exporting to file formats which support marker data.)
• --omitDendMarkers.  (Omits markers which are associated with dendrite structure. Only relevent when exporting to file formats which support marker data.)
• --omitAllSpines.  (only relevent when exporting to file formats which support spine data).
• --omitGlobalSpines.  (Omits spines which are associated with specific soma or tree structure. Only relevent when exporting to file formats which support global spine data.)
• --omitDendSpines.  (Omits spines which are associated with dendrites. Only relevent when exporting to file formats which support spine data.)
• --omitAxonSpines.  (Omits spines which are associated with axons. Only relevent when exporting to file formats which support spine data.)
• --moveOriginToSoma (will translate the entire neuron so that the origin (0,0,0) is at the mid-point of soma samples - or tree roots, if there is no soma.  Overrides --translate).
• --forceSphereSoma <diameter>  (will replace any existing soma data with a sphere representation of the specified diameter).
  
• --forceCylinderSoma <diameter> <radius>   (will replace any existing soma data with a single uniform segment of specified length and diameter).
• New export options
• --versionNumber <version>
  
• MorphML:  any valid version number from '1,0' onwards (excluding alpha/beta versions):   '1.0', '1.1', '1.2', '1.3', '1.4', '1.5', '1.6', '1.7', '1.7.1', '1.7.2', '1.7.3', '1.8.0', '1.8.1', '1.8.2' (default), '2.0' (experimental - may not be completely correct)
• No other formats are relevant for this option yet, but some could be added in the future (possible candidates are NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML)
  
• --style <style>.  (Allows some fine-tuning of the export format. Ignored if the specified style is not relevant to the specified export format. Different styles are just different but equivalent ways to represent the same data, within the scope of the format specification).
  
• NeurolucidaASC:
  
• 'modern'  (default).   Comments describe full tree path from root branch, but only for first sample of each sample list. Remaining samples have a comment indicating sample number.  (As generated by recent versions of Neurolucida).
• 'classictags'   Each sample has a comment giving full tree path from root branch. (As generated by eariler versions of Neurolucida)
  
• 'verbose'   Same as 'classictags', but with associated NeurolucidaClassic tags removed. (As generated by eariler versions of Neurolucida)
• 'nocomments':   No comments are generated (except for header), otherwise layout of file is as 'modern'.
  
• 'compact':   No comments, and reduced whitespace usage (maintains indented layout for readability).
  
• 'nmpml':   As 'compact', with same header as nmpml-generated ASC files.
• NeuronHOC:  (***PARTLY DISABLED PENDING SOME FIXES***)
• 'swc2hoc'  (default) (same style as generated by SWC2HOC.AWK script)
• 'ntscable'  (same style as generated by NTSCable v.2.0)
• 'slsr' (ref: )
  
• 'cnic'  (**to check**...same style as found in CNIC database - similar to SWC2HOC, with dendrite segments named 'dendrite' instead of 'apical' or 'basal')
• 'geometry_to_neuron' (as generated by geometry_to_neuron.py script - ref: )
• 'Oz_neuron'  (same as geometry_to_neuron, with soma data located before tree data, instead of after - Oz_neuron.py script.  ref: )
• 'topol'  (commonly used style, with proc topol() describing connectivity and sample data.)
  
• 'morphmlxsl'  (same style as produced by MorphML_v1.8.1_NEURON.xsl)
• Additional styles may be implemented on request (just ask!)
  
• NeuroZoom:
• 'longpath'  (default)  (each tree contour ends at a tree terminal point, spanning branch points where necessary)
  
• 'shortpath' (each tree contour corresponds to an unbranched dendrite section, and does not cross branch points).
  
• SWC:   (Note that 'gulyas' is not included as an export option, due to cumbersome id-diameter mapping.)
• 'stdswc' (default - standardised SWC format, as used by NeuroMorpho.org).
  
• 'cnicswc'. (similar to standard, except structure ids 5, and 6 are used to explicitly identify branch points and terminals).
  
• NeurolucidaDAT
• 'badmarkersize' (default - marker block sizes are not actually correct in the format generated by Neurolucida software - and this also distorts the sizes of blocks in which markers are embedded.).
  
• 'corrected' (experimental - this calculates the correct marker block sizes. Needs to be thoroughly tested with Neurolucida software, but is hopefully ok, as long as these sizes are probably not actually essential for correct import.)
  
• No other formats are relevant for this option.
• --colorXXXX  <Colour> | RGB(R:G:B)   (Colour setting, for formats which support such data - NeurolucidaASC, NeurolucidaDAT, NeurolucidaXML, NeuroZoom. Note American (color) or British (colour) spelling permitted). Applied to all elements of specified type, i.e. currently there is no fine control.).
  
• --colourSoma, --colorSoma  (default: Blue)

• --colourDendrites, --colorDendrites (default: Green)

• --colourAxons, --colorAxons (default: Red)

• --colourSpines, --colorSpines (default: Yellow)
• --colourMarkers, --colorMarkers (default: Orange)
• possible colours by name:  Red, Green, Blue, Yellow, Cyan, Magenta, White, DarkRed, DarkGreen, DarkBlue, DarkYellow, DarkCyan, DarkMagenta, Orange, MediumGray, BrightGray, SkyBlue, MoneyGreen, Cream.  This list is based on the named Neurolucida colours, but can also be specified if the export format is NeuroZoom, where they will be interpreted as 16-bit per channel RGB values.
  
• If specified as RGB,  each channel is 8-bit, i.e. from 0-255. For NeuroZoom format, the export will rescale these to 16-bit.
  
• --setPrefixAxon <string>  (Use this to overide default axon structure identifier. Relevant for Eutectics (default "ax"), Genesis (default "a"), MorphML (default "axon_group"), NeuroZoom (default "axon"), PSICS, NeuronHOC)
  
• --setPrefixDend <string> (Use this to overide default dendrite structure identifier. Relevant for Eutectics (default "d"), Genesis (default "d"), MorphML (default "dendrite_group"), NeuroZoom (default "dendrite"), PSICS, NeuronHOC)
  
• --setPrefixSoma <string> (Use this to overide default soma structure identifier. Relevant for Eutectics (default "cell"), Genesis (default "soma"), MorphML (default "soma_group"), NeuroZoom (default "soma"), NeurolucidaXXX (default: "CellBody") , PSICS, NeuronHOC).
• --identifyNL  (where a file format supports comments, a comment will be generated which identifies NLMorphologyConverter as the creator)
• --cellName <name> (assigns a name to the cell - only relevant where a file format supports comments, or a specific mechanism for naming the cell.)
• --addComment <string>  (for suitable formats, add arbitrary comment).
  
• Testing regime:
• Updated to use new data in neuromorpho.org archive version 4.0.
• Added more MorphML (NeuroML Level 1) test data.
• Added a collection of Neuron hoc files, in various styles, in order to test the new NeuronHOC importer (mainly sourced form ModelDB database -> http://senselab.med.yale.edu/modeldb/)
  
• Added more Genesis test data (also sourced from ModelDB database).
• Introduction of format style variations allows much better test coverage of all multi-style formats  - tests all supported export styles and version numbers of a specific format.
  
• Soma data included in test, wherever data+formats are compatible enough.
• Marker data included in test, wherever data+formats are compatible enough.
  
• Spine data included in test, wherever data+formats are compatible enough.
  
• Added new test which compares data already available in multiple different formats (i.e. has not been generated by NLMorphologyConverter, e.g. from the CNIC archive, or using MorphML xsl to convert to Neuron or Genesis formats.).
• Implemented a small set of tests using manually calculated properties of the data, covering most formats, and which aim to compare imported data with known properties of the data.
• All 13,000+ test files pass the current testing regime.
• Note that NLMorphologyViewer has been updated (version 0.3.0) to display marker and spine data, as well as additional soma, tree, marker, spine, and global statistics.
• Note that various format specifications have been updated on the website (fixes, and additions).
  
• Note data which is not currently conserved when converting between NeurolucidaDAT, NeurolucidaASC and NeurolucidaXML formats. To preserve this data, use Neurolucida software to convert between these formats. (Some of this information may be preserved in future versions.)
  
• Sections, ImageCoords, Description, Thumbnail, Text data blocks.
  
• Resolution, Varicosity, Style, + more properties.
  
• Contour, tree, and marker Colours. (However, export colours can be explicitly specified).
  
• Tree terminal type.
• Dendrite Type (Apical or Basal).
  
• Non-soma contour data.
  

• 0.8.1 - 10th August 2009 
• Windows/MacOSX release (mostly fixes for bugs found since obtaining a larger set of NeurolucidaDAT test files.  IMPORTANT - exported NeurolucidaDAT data has not been tested directly with Neurolucida software. Please report any problems using the generated data.).
  
• Fix for NeurolucidaDAT import (text label data was not handled properly).
  
• Fix for NeurolucidaDAT import (occasional incorrect handling of data footer).
  
• Fix for NeurolucidaDAT import (erroneous marker data size was not always correctly worked around).
• Fix for NeurolucidaDAT import (cannot skip contours which contain marker data - erroneous marker data size forces all contours to be parsed completely).
• Fix for NeurolucidaDAT import (big-endian fixes - however import/export on big-endian mac systems has still not been tested).
• Fix for NeurolucidaDAT export (always add an empty Sections group block, even though we don't have Section data).
• Fix for NeurolucidaDAT export (always add a 64x64x4 image block, directly after Sections group block).
• All test files pass current testing regime.
• Fix for command line options
  
• MacOSX  --report option bug fixes.
  

• 0.8.0 - 7th July 2009
  
• Windows only release. Other platforms will be updated as soon as time permits.
  
• Windows installer improved - allows user to choose installation location, and will gracefully upgrade older versions.
• Windows installer - executable installation directory no longer added to system PATH environment variable. Until this is fixed, invoke the command using the full path, or add installation directory to the PATH manually (Control Panel -> System ->  Advanced -> Environment Variables -> Edit "Path" system variable..)
  
• Installation now includes latest PDF format user manual.
  
• Neurolucida support reorganised - NeurolucidaV3 renamed to NeurolucidaASC.  Support added for binary format NeurolucidaDAT (both import and export)
  
• Note this is the first binary (non-text) format to be supported.
  
• DAT support is still experimental, with only a small number of original datafiles available for testing. Please get in touch if you have problems.
• DAT support has not been tested on big-endian Mac systems (power pc+MacOSX). Endian-swapping support is included, however, and in theory should work.
  
• DAT export does not yet support marker data (import does support markers).
  
• Fix for NeurolucidaASC import (Soma data was ignored in some cases.)
  
• Fix for NeurolucidaASC import (Multiple soma contours no longer merged)
  
• Fix for NeurolucidaASC import (Now accepts Neurolucida files generated by nmpml translation system)
• Fix for Eutectics export (Upper limit of  999.9 um on output diameter values).
• Fix for SWC import (Soma data not correctly imported for some files. Still problems with Gulyas variation of this format).
• All test files pass the current testing regime. (updated to include new files in NeuroMorpho 3.2.  10,000+ files in total.)
• Fix for command line options
  
• --warnings  bug fixes

• 0.7.0 - 4th January 2009  (**updated - 31st January)
  
• Win32/Linux release only.  **Mac OSX version available since 31st January. **Linux version reverted to 0.6.3 temporarily.
  
• New command-line options
  
• --report <filename>  (generates a report detailing:  import, modification, export, statistics, warnings).

• --verbose (provides additional commentary on import, modification and export ).

• --merge <filename> [modify options] (the neuron data file specified will be merged, subject to the modify options specified:  omit*, flipTreeType, all*, scale, translate, rotate, are valid).  Note that when using merge, you need to use the --export option to specificy the output file and format.
  
• --split <filenameprefix> <filenamesuffix> (each tree is exported as a file with name <filenameprefix>_dend_XX.<filenamesuffix>, or ..._axon_XX...)

• --omitMarkers  (marker points are not exported - only relevant for those formats which support markers)
• --rotate <x y z Angle> (will rotate entire neuron around direction vector (x, y, z) by "Angle" degrees)
• Updated command-line options
  
• --stats  (new stats added)
• tree surface area
  
• tree volume
• maximum terminal distance (physical, not path)
  
• --warnings (new warnings added)
• unusually large change in diameter
  
• large terminal diameter
• unusually long section
• unusually short section
• intersecting sections
• encapsulated branch (the entirity of a child branch lies within the extent of the parent branch)
  
• --help  (updated to reflect new/modified options)
• --import option removed (redundant)
• Fix for NeurolucidaV3, NeuroZoom (marker points retained and exported)

• 0.6.3 - 28th October 2008
• Bug-fix release only. Win32/Linux only (no access to Mac hardware)
• All test files (more than 9000 in total) pass the current testing regime.
• Fix for NeurolucidaV3 import (problem with previously unseen marker shapes)
  

• 0.6.2 - 30th May 2008
• Bug-fix release only. All platforms (Win32/MacOSX/Linux).
• All test files (more than 5000 in total) now pass the current testing regime.
  
• Reverse previous erroneous fix (v. 0.6.0) which assumed NeurolucidaV3 used radius, not diameter to represent thickness. In fact, NeurolucidaV3 uses diameter, while SWC uses radius. All supported file formats have now been checked to confirm whether or not they use radius instead diameter to specify thickness. The import and export algorithms for the file formats which use radius have been fixed (only two - SWC, LNeuronAmiraMesh).
  
• Fix for SWC import (more reliable checking for non-standard SWC tag numbers)
  
• Fix for SWC import (various other little improvements to importer to cope with non-standardized data - copes with all data in the testing regime. Still potential pitfalls, but difficult to improve more due to arbitrary way structure tags can be used.)
• Fix for SWC export (all soma samples had same co-ordinates/diameter - that of the first sample).
  
• Fix for NeurolucidaClassic import (in some cases, a short 2-sample dendrite was given an unnecessary extra duplicate sample point).
  
• Linux - fix for command line options (scale, translate)
• OSX - fix for command line options (omitAllAxons, omitAllDends, allDendsAsAxons, allAxonsAsDends, omitTrees, flipTreeType)

• 0.6.1 - 22nd May 2008
• Bug-fix release only. All platforms (Win32/MacOSX/Linux).
• Note that certain command line options are currently disabled for OSX (omitAllAxons, omitAllDends, allDendsAsAxons, allAxonsAsDends, omitTrees, flipTreeType) while others are disabled for Linux (scale, translate). This is due to compilation issues on these platforms.
  
• All test files (more than 5000 in total) pass current testing regime, except 1 SWC file. However, there are also definitely still some other issues with the import of certain non-standardized SWC files.
  
• Fix for SWC import (representation of values of 1000 or more, e.g. 1,005.66, in a very small number of test files - comma caused incorrect import of corresponding branch data).
• Fix for SWC import (place upper limit of 99999.0 on co-ordinate and diameter values so that all supported export formats can cope).
• Fix for MaxSim import (incorrect connectivity was generated when 2 sample points are directly connected branch points).
• Fix for Eutectics import (algorithm was creating unnecessary new branch for some incompleted branch points when the expected branch data didn't follow in the data file, and a new object started instead.)
• Fix for NeurolucidaClassic import (first samples of child branches were incorrectly assigned sample of parent branch end sample, rather than the sample value in data file.)
• Fix for NeurolucidaClassic import (terminal move-to points are over-ridden by an immediately following branch move-to point at the same location - req. e.g. for n262.asc)
• Fix for NeurolucidaClassic import (accept minor value of  n as well as n+1 (where n is structure id) in line-to points - req. for n142.asc).
  
• Fix for NeurolucidaClassic export (first sample of child branch incorrectly set as parent end sample, rather than the actual stored first sample value, causing occasional inconsistency.)

• 0.6.0 - 19th May 2008
• All platforms release (Win32/MacOSX/Linux).
• Warning - this version seems to have taken a backwards step in non-standard SWC and NeurolucidaClassic support.  Issues will hopefully be resolved in an upcoming minor release sometime this week.
  
• MorphML import/export re-activated.
• Testing regime now includes MorphML and MaxSim formats.
• Fix for MorphML export and import (complete re-implementation.).
• Fix for MaxSim export (sample points internal to a branch segment could sometimes be missing.)
• Fix for SWC import (handle non-standard SWC structure numbers more gracefully).
• Fix for SWC import (handle unexpected changes in structure, and odd connectivity between structure, more gracefully).
• Fix for NeurolucidaV3 import and export (this format actually uses radius, not diameter).
• Added initial support for NeuronJ ndf format.
  
• This is a 2D line-tracing format, and only import functionality has been implemented.
• All sample z-components are set to 0.0.
  
• All sample diameters are set to 1.0.
  
• Pixel-based (x,y) co-ordinates need to be scaled by user to microns using --scale option.
  
• Added lots of usage flags to provide more useful output, and to give some control over the structure which is exported.
  
• --import <filename>

• --stats (Currently displays the following data, both for entire neuron and per-tree)

• number of sample points
• number of branch segments
• number of branch points
• branching order
• number of terminals
• maximum terminal path distance (microns)
• total tree branch length (microns)
  
• --warnings (Currently detects the following...)

• tree root too distant from soma
• unary branch point
• non-binary branch point
• disjoint branch connection
• branch has zero samples
• branch formed from only one sample
• sample diameter is too large
• sample diameter is unusually small
• sample diameter is zero
• --export <filename> <fileformat> 
• --omitSoma
• --omitAllAxons (disabled on OSX this release)

• --omitAllDends (disabled on OSX this release)
• --allDendsAsAxons (disabled on OSX this release)
• --allAxonsAsDends (disabled on OSX this release)
• --omitTrees <comma_delimited_list_of_tree_ids> (disabled on OSX this release)
• --flipTreeType <comma_delimited_list_of_tree_ids> (disabled on OSX this release)
• --scale <scale_x_axis> <scale_y_axis> <scale_z_axis> <scale_d> (disabled on LINUX this release)
• --translate <value_microns_x> <value_microns_y> <value_microns_z> (disabled on LINUX this release)

• 0.5.0 - 24th April 2008
• Initial Linux (x86) release.
  
• Fix for Nevin export and import (copes properly with the different ways in which soma and dendrite root point data is organised).
  
• Fix for NeurolucidaClassic import (now copes with spurious Move points, incompleted Terminal points, and soma data with missing Section Change start point).
• Fix for NeurolucidaV3 export (guarantee at least one space between sample point data values - x, y, z, d).
• Fix for NeuroZoom import (connectivity error where arbors directly connect to the end of other arbors).
• Fix for NeuroZoom import (now correctly handle arbors which attach to an arbitrary point of a previous arbor - i.e. unordered data, to the extent this format allows).
• Fix for GulyasTree import (place sensible limits on sample point co-ordinate values, to cope with some odd data).
  

• 0.4.0 - 15th April 2008
• It is no longer possible to export neurons with non-binary trees to formats which only support binary trees.
• More intensive testing regime - Introduced asymmetric import/export/re-import. Most fixes detailed below are a result of this testing.
• Fix for multiple formats (Oxford, NeurolucidaClassic, NeuronNTSCable, Glasgow) export (fixes crash when neuron has no soma data).
• Fix for multiple formats (All) import (Unary branch points are collapsed to clean-up internal data structures and help with automated testing).
• Fix for Eutectics import (safely ignore BTO, TTO tags).
• Fix for Eutectics export (Make sure soma data is always terminated with SOE, even if there is only one soma point).
  
• Fix for NeuroZoom import (Now safely deals with an arbor which is attached to the end point of another arbor.)
• Fix for NeuroZoom export (Non-binary tree properly exported)
• Fix for NeuroZoom export (Axon data now exported)
  
• Fix for SWC import (various fixes related to incorrect usage of soma point as a dendrite point, and soma-less data. As a consequence, for the moment any tree with a branching root point will be split into multiple trees).
• Fix for SWC import (now correctly ignores lines which contain only whitespace)
  
• Fix for SWC export (now exports axon data and sets structure id properly)
  
• Fix for NeurolucidaClassic import (minor improvements to file parsing)
• Fix for NeurolucidaV3 import (fix for algorithm that checks sections are valid.)
  
• Fix for GulyasTree import (correct determination of root branch points when samples are different)
• Fix for Oxford export (Diameter values >= 10.0 were incorrectly formatted or caused a crash)
• Fix for Glasgow export (Axons exported)
• Fix for NeuronNTSCable export (fix for when soma is missing)
• Fix for Douglas3D export (Soma data forced to have minimum 3 data points, and therefore at least one scp).

• 0.3.0 - 25th March 2008
• NLMorphologyConverter is now subject to an intensive automated testing regime.
  
• Fix for SWC import (ignore lines beginning with *, to cope with a custom SWC format)
• Improvements to Nevin autodetection
• Fix for NeurolucidaV3 import (safely ignore any unknown top-level keywords - fixes crash)
• Fix for NeurolucidaV3 import (safely ignore any unknown terminal types - prevents early terminaion of import)
• Fix for NeurolucidaV3 import (added more marker shapes, preventing data corruption)
• Fix for NeurolucidaV3 import (Spines no longer cause import to stop early, but spine data is still ignored for now)
• Fix for NeurolucidaV3 import (Occasional marker data read bug causing early termination of import)
• Fix for NeurolucidaV3 export (crash when no soma exists in data)
• Fix for NeurolucidaV3 export (tree depth whitespace corruption issue)
• Fix for Eutectics import (more generalised - doesn't assume particular naming convention for dendrites)
  
• Fix for Eutectics export (MTO sample point number wrong by -1)
  
• Added initial support for AmiraMesh (as exported by L-Neuron), and Gulyas' Tree format
• Initial support for a generic neuron hoc morphology importer (NeuronGeneric). ***Import is very limited at the moment.

• 0.2.0 - 13th March 2008
• Initial Mac OSX version. 
• Fix for NeuronSWC2HOC export bug (incorrect dendrite count).
• Fix for NeuroZoom export bug (connection node wrong by +1).
  
• Fix for NeuroZoom import bug (non-binary branch points).
  
• Fix for Eutectics export bug (disappearing "-" sign issue)
• Fix for NeurolucidaV3 import bug ("Font" keyword)
• Fix for NINDS3D import bug (don't generate fake soma point!)
• Genesis export disabled (new data highlights new problems)
• Todo - certain formats do not support binary trees, but there is currently no mechanism in place to prevent export of non-binary trees to a binary-only format...
  

• 0.1.0  - 10th March 2008
• Initial public release (win32)