Change Log v1.7

• Modified the formula for fractal dimension to Σlog(1+x)(1+y)/Σlog(1+x)^2 where x is Euclidean distance and y is path distance.

Bug Fixes for L-Measure v5.2 (06/24/2014)

• This bug fix is applicable only for command line execution or batch processing of large #swc files. The executable is crashing when parsing files with spaces, this has been fixed by allowing the use of (a) ‘*’ to replace space or (b) use quotations to enclose the file name including the path.
  For example:
  Lm.exe -f0,0,0,10.0 -sC:\Users\user1\Desktop\Lmv5. 2\Lmout.txt C:\Users\Romil\Desktop\Lmv5.1\v*e_moto1.CNG.swc
  OR
  Lm.exe -f0,0,0,10.0 -sC:\Users\Romil\Desktop\Lmv5.1\Lmout.txt "C:\Users\Romil\Desktop\Lmv5.1\v  e_moto1.CNG.swc"
• For computing the soma surface area, Surface_area, section area and volume at the tree level, the PI value from the inbuilt C++ library value(M_PI) is used instead of a hard coded two decimal constant value.

• LM uses swc format natively for processing the data or for swc conversions. The original reference for SWC format is described here by its inventor, Robert Cannon.
• More information related to SWC format including the convention followed for arbor type description is found here:
  http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html
  http://research.mssm.edu/cnic/swc.html

Change Log v1.6

Bug Fixes/New Features for L-Measure v5.1 (01/24/2014)

• Added configuration file to the Online L-Measure deployment process. This allows de-coupling the hardcoded paths from the code making the deployment process independent of the host machine environment.

• Fixed the online Applet version crashing issue. This fix will now filter out the file names with special characters like Ð,Ñ,Ä,† etc. The GUI will not accept the files with these special characters.

Change Log v1.5

Bug Fixes/New Features for L-Measure v5.0 (02/15/2013)

• The acceptable format of an input SWC file is one which has 7 colums of data namely id, type, x, y, z, radius, pid. If a file has additional columns then it will not be processed and display an error message on the GUI.
• Fixed the online version crashing issue. This fix will now filter out the incompatible input file formats both by checking the file extension and the internal structure. Currently swc, neurolucida and amira versions are the most commonly used formats.
• Fixed the Bif_ampl_local angle, which is giving negative values for some of the files. This issue also has been fixed after removing the decimal point precision.
• Fixed the PCA orientation of the neurons such that when Z-resolution is too low, the swc files will be oriented based on only two components (X and Y). This will avoid the swc conversions to orient files that have low resolution jagged looking Z direction in the XY view. This fix, first tests for Z-resolution by checking whether as much as 30% of the z coordinates are same, if true, then the PCA is done only on two axes (X and Y), in the second part of PCA, the orientation is also done based on just two components. For implementing this logic that can conditionally skip Z-coordinate, three new functions ZresolutionEstimator, saveZcoords and setZcoords are implemented in Neuron.cpp and additional data structures like 'datacopy' array and flags like 'zresolution' were created in pca() method. The fix has been tested on the entire Brunjes archive, which was visually verified in CVAPP. Further, entire NMO data was tested in extracting morphometrics using PCA.
• Fixed Bif_ampl_remote angle by removing the decimal point conversion. Only metrics that are a ratio (e.g. Taper_1, fractal, etc) or length are converted to have decimal point precision. This fix eliminated outlier angles that are too large.
• Replaced + with * in the file path in Neuron.cpp and Morph.cpp, this will now allow the users to choose folders that have a '+' in the path.
• Fixed two linux compiler related bugs. one in converting Neurolucida files to swc in neuron.cpp in the lookFor(tag,in) method. second, in the bif_torque_remote method to initialize prev_next1 and prev_next2 to NULL
• Fixed ~Neuron() code to ensure all segments are deleted and memory is freed. Updated revision# in morph.h; made changes to Helix, Bif_ampl_local, Bif_ampl_remote functions in Func.h to restrict decimal points to 2 digits.
• Fixed the code to filter invalid file types for input neurons. Made changes to the LookForFileType() function to correctly identify .swc files and to filter out other invalid file types.

GUI v5.0

• Two different versions of the lmeasure executable are made available for 32-bit and 64-bit Linux operating systems.
• A new FAQ has been added to the install.html to mention the valid SWC input file parameters. FAQ
• Added the svnRevision entry to the properties file. This will reflect the latest code revision of LM GUI, which is intended for development purposes.
• Added the code to calculate the version number using the svnRevision entry from the properties file.

• Corrected code for placing the LMSearchin.txt and LMSearchout.txt in the proper session folder in online version. This is desired to keep log of all LM input files systematically inside the corresponding session folder.
• Changed the logUrl entry in the properties file to point the online version to the correct location. This will also ensure that all the session folders are created in the designated folder that is assigned to logUrl.
• Changed the code for ‘Analyze Subtrees’ option both in the local and online versions. This fixed the ‘subtree analysis’ function and synchronized with the ‘subtree generation’ option too. Both options, now refer to the subtrees saved into Apical, basal and axon folders.
• Modified the code to replace space (“ “) with star (“*”) in the pathname of an input SWC file. This will allow the user to have ‘+’ symbol in the input file path.

Change Log v1.4

Bug Fixes for L-Measure v4.0 (06/13/2012)

• Terminal branches are considered for all Bifurcation remote angles (Bif_ampl_remote, Bif_tilt_remote, Bif_torque_remote). Previously, remote angles were computed only between bifurcating nodes, this fix includes terminal branches also by considering the tip nodes.
• RAW data values are printed for double distribution selection. Previously, the raw data values were printed only for single function, this fix allows printing for double distribution also.
• L-Measure code has been fixed to make it robust enough to accept and process large neurons. Largest file tested so far is ~10MB SWC file, but it can process even larger files.
• Daughter_ratio and Pk_classic have been fixed. The functions were returning invalid results when the input file has zero diameter.
• Fragmentation and Taper_1 were made consistent with contraction and Taper_2 respectively. Previously, Fragmentation and Taper_1 were skipping the stem branches, hence the stem compartments were not included in the results.
• Height, Width, Depth functions code has been fixed. Previous version was not using all the points in the SWC for calculation of the result.
• L-Measure was crashing when doing PCA analysis on width, height and depth measures for neurons that has type = 3 or type = 4 (dendrites) defined, but not type = 1 (cell body). This has been now taken care and the code accepts such data without crashing.
• modified FAQ#10 about PCA.

L-Measure v3.8 & GUI v4.4 (03/23/2011)

      LMv3.8

• Important changes are made to soma representation in the LM converted SWC formats. Please refer here
• Input files that have soma as a single point will be converted into 3 point soma (cylindrical representation). The changes will be reflected in ‘SWC conversion’ selection in the output panel
• Neurolucida files that have soma as single contour will also be converted to 3 point soma. The first point in the newly converted SWC file is the average of all the points in the single contour.
• Neurolucida files that have soma as multiple contours will be converted into multiple point cylindrical soma where each contour is averaged to one soma point.
• The soma_surface function will remain unaffected since the formula for area and sphere and cylinder are adjusted to return the same surface area. The height of the cylinder is set to 2*radius of the sphere. The files in NeuroMorpho.Org are converted and tested for this change.
• All functions are synchronized with the same default specificity condition, which is type > -1. Any specific conditions can be selected in the specificity panel for desired function(s). see the related FAQ
• AmiraMesh v1.0 format to SWC conversion now supports reconstructions with zero diameters also. This has been tested on automated reconstructions of fly neurons that will be made available on NeuroMorpho.Org, with a constant diameter of 0.5µm
• New command line option “-dx.xx” is introduced in L-Measure for SWC conversions (Amira to SWC only). This allows the user to enter his/her choice of diameter values e.g., –d2, -d3.5, –d0.03467, etc.
  Example : -sZ:\Soumya\Test+Folders\Amira+Conv+Problem_07202011\windows\Lmout.txt -C -p –d0.03467 Z:\Soumya\Test+Folders\Amira+Conv+Problem_07202011\windows\12070404c1.am

      LMv3.8

• The output of height/width/depth is made consistent. Now, the total_sum/max/min/avg all returns the same value. This is because these three functions are calculated at the entire arbor level. Hence only one value.
• The time of execution for each neuron is logged in the err.txt file as “Current local time and date:Thu Dec 01 13:51:38 2011”. The err.txt file is created by the standalone version in the same location that LM executable is located.
• The ‘Generate Subtrees’ option will generate and organize the subtrees into Axon, Basal and Apical folders locally.
• Bif_ampl_local angle at the soma is now changed to return the maximum angle between the soma and one of its stems.
• A new comment header will be added to the Neurolucida to SWC conversions to add details about cell body representation in the original files.

      GUI v4.4

• The GUI code was changed to support the new sub tree generation functionality. The online GUI can categorize generated sub trees into Axon, Basal and Apical.
• LMSearch panel in GUI v4.3 is added with a “remove all” button. This button will remove all the files from the input file chooser window.

      LMv3.8

• The Bifurcation angle functions were giving erroneous values (value above 360 deg. and sometimes NAN/not a number). This has been fixed now.
• The N_Branch = N_bifs+ N_tips. The functions is edited to return a number same as N_bifs + N_tips. See FAQ related to this. The comments printed in the SWC converted files were having extra empty lines in some cases. This has been fixed.
• The SWC conversion of the files that are having soma in the middle (as opposed to the beginning of the file), did not rearrange the soma to the top. This has been fixed. In Linux version sometimes the multiple files are not getting converted at one go. This has been fixed with a minor change in the code.
• N_stems code is fixed. Previously, the function would count change of type anywhere in the tree. But this is now fixed according to the definition (see help) to return stems (different types) only near the soma area.

      GUI v4.4

• The GUI Search panel’s “load to group2” click was failing. This has been fixed. Also when “load to group2” is clicked the stat_tests checkbox is automatically highlighted in both function and input panels.

• What is the maximum number of files which can be used in online L-Measure?
• The online L-Measure is not initializing in Linux based OS browsers?

L-Measure v3.7.1.1 & GUI v4.3 (11/18/2011)

• The FAQ How can we verify the result of N_Branch? has been changed.

• The N_branch function giving wrong value for cells with no soma.

L-Measure v3.7.1 & GUI v4.3 (07/27/2011)

• The FAQ has new update.
  • Which compartment types are accepted by L-Measure?
  • What happens when there is no Soma in the input file?
  • Why do I see negative value for taper?
  • Is SWC file with more than one soma compartment accepted by L-Measure?
  • How does LM compute Taper_1 for bifurcations where the parent and daughter compartments don’t change in diameter?
  • Why is PCA conversion crashing?
  • Is Does Taper_1 considers terminal segments?
  • How can we verify the result of N_Branch?
• LM Help has new updates.
  • New help page for command line usage.
  • New note added to Taper_1 function.
  • Grouped the LM metrics under different headings based on their function and return values

      LMv3.7.1

• The SWC to SWC conversion is missing the required comments in the header section of the resulting file. This has been now fixed
• Taper_1 formula is changed to parent minus child diameters instead of the opposite Please refer to the function page for more detail
• Taper_1 function logic is changed. It is now considering the terminal branches also
• Fractal Dimension function was crashing on selection of multiple files in the Windows version of LM. This has been now fixed.
• N_Branch function logic is changed. N_Branch = N_Stems + N_Bifs + N_Tips. However if there is more than one soma segment, then, N_Branch > N_Stems + N_Bifs + N_Tips.
• The SWC conversions w/PCA will not be supported for files that don't have a soma point.
• Amira to SWC file conversion was incorrect in Linux version. This bug has now been fixed.
• Changed the computing condition for PK, PK_2, PK_classic, Rall_power, Bif_tilt_remote, Bif_tilt_local, Bif_torque_local, Bif_torque_remote such that the total #compartments do not include soma/virtual compartments.

      GUI v4.3

• When the files from LMSearch panel were loaded to Input panel, the count of files label was not incrementing. This has been now fixed.
• The file chooser window in the input panel had a bug. The logic of code was changed and is fixed.
• File chooser of LMSearch panel was not selecting files input files from subdirectory. The code changes are made and the problem is fixed. The count of the files is also being shown in the panel.
• In LMSearch panel when the load to group 2 is done the stats check boxes are selected automatically in the Input and Function panels.
• If Stat check box is selected/deselected on Input panel the same action will take place in function panel.
• The WRL and DXF functionalities were not working for the online version. These two functionalities have now been activated.
• LMSearch panel was not working for the online version. This has been not fixed.

L-Measure v3.7 & GUI v4.2 (05/24/2011)

      LMv3.7

• WRL Conversion function has been added to the Linux version.
• DXF Conversion function has been added to the Linux version.
• LM will accept Input neuron file with unlimited comments (lines starting with “#”).
• All SWC and PCA conversions will return x, y, z values of segments truncated to 2 significant digits.
• The computation of the Fractal Dim is changed. Now is calculated using the formula for slope (b) = (NSXY - (SX) (SY)) / (NSX2 - (SX) 2), where X is the Euclidean distance and Y is the path distance. Please check help doc for more details.

      GUI v4.2

• Input to L Measure GUI will consider the the sub folders and files of the selected folder.
• Input panel will accept the files types swc, SWC, txt, TXT, asc, ASC, am, AM only.
• Input Panel shows the count of files selected.
• The SD of Stat Test is removed from function tab.
• New version of Help Released.
• Double distribution supports function both in A vs B and B vs A format.
• New check boxes for WRL and DXF Conversion options on GUI.

      LMv3.7

• PCA conversion was not working. This has been now fixed.
• ASC to SWC conversion was missing the dendrites and soma parts. This has been now fixed.
• Small fix done to enable SWC conversion of Amira files.
• In SWC conversion, the newly added virtual soma is set to type = -1.

      GUI v4.2

• L Measure GUI works fine on Windows 7 & Vista.

• Added new tags for parsing cell body parts in the NeuroLucida reconstructions to generate SWC converted files for the ‘swc conversion’ feature in the output tab.
• Modified the computation of Width, Height and Depth metrics in the function panel for the given set of input neuron(s).
• Added FAQ to facilitate ease of use of L-Measure
• Added Bug Tracker feature to allow users track a specific bug or report new issues.

• Resolved the multiple file analysis issue where L-Measure was crashing when multiple files were input.
• Resolved the issues for SWC file conversion and metric extraction for files that have soma located in the middle and/or has more than one soma compartment.
• The GUI has been fixed as it was not selecting the Amira files with .ama extension.

• Mac Version: Mac version of L-Measure.
• Added FAQ to facilitate ease of use of L-Measure
• Added Bug Tracker feature to allow users track a specific bug or report new issues.

• Implementation of Width, Height and Depth metrics based on specificity. However the total_sum value of these three metrics must be disregarded. The #compartments considered gives the actual no.of compartments considered from specificity. Min or Avg or Max values can be considered for analysis. Please look at online help on these metrics for details.

• File Size Issue: LM was not able to handle single larger file size (greater than 4MB). This bug is fixed in this newer version.
• Conversion Issue: In the previous version while converting from ASC to SWC, file would add spine block to the coverted file. So we have re-modified the code so that it will skips spine blocks from the ASC files.
• Width, Height and Depth issue: In the pervious version for a analysis of multiple files the functions like Width, Height and Depth were getting the same values i.e. the value of the first file which was analysied for the rest of the consequent files. Made changes so that we can get different values for the Min, Avg and Max for different files with or without specificity
• In the GUI to avoid a selection of 'Global' option of Input Panel whenever a mouse pointor goes over it.
• LM would add extra segment with branch order of value '0' to the branch order matrix made the necessary change in the matrix to fix the bug
• LM would automatically select 'Global' paramater for a larger filepath (more than 150). Made the necessary changes in the code for selection of larger filepath
• GUI had an extra text field in the output panel. Removed it from the GUI
• In SWC conversion in removing the comment section and removing extra new lines in the converted file.
• In SWC conversion in removing the comment section and removing extra new lines in the converted file.