Release Notes for L-Measure v5.

3 (06/07/2016)

Bug Fixes for L-Measure v5.3

Lmv5.3

Bug Fixes
 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

Lmv5.2

Bug Fixes
 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<space>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.

Help doc

 LM uses swc format natively for processing the data or for

swc conversions. The original reference for SWC format is
described here
(http://www.sciencedirect.com/science/article/pii/S016502709
8000910) 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
Release Notes for L-Measure v5.1 (01/24/2014)

Bug Fixes/New Features for L-Measure v5.1

Lmv5.1

New Features

 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.

GUI v5.1
Bug Fixes

 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

Bug Fixes/New Features for L-Measure v5.0

Lmv5.0

Bug Fixes
 The Accepted format of an input SWC file is one which has 7
columns 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. Cur-
rently swc, neurolucida and amira versions are the most com-
monly used formats.
 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.
 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 orienta-
tion is also done based on just two components. For imple-
menting 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 'zresolu-
tion' 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.
 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 neu-
rons. Made changes to the LookForFileType() function to cor-
rectly identify .swc files and to filter out other invalid
file types.

GUI v5.0
New Features
 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.
http://cng.gmu.edu:8080/Lm/FAQ/install.html#LM5.0_1
 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.

Bug Fixes
  Corrected code for placing the LMSearchin.txt and LM-
Searchout.txt in the proper session folder in online ver-
sion. This is desired to keep log of all LM input files sys-
tematically inside the corresponding session folder.
 Changed the homeUrl 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 des-
ignated folder that is assigned to homeUrl.
 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’ op-
tion 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.

Bug Fixes for L-Measure v4.0

 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.
(please go to FAQ#10 for details about PCA).

New Functionalities for L-Measure v3.8

Major changes:

 Important changes are made to soma representation in the LM

converted SWC formats. 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. Please
refer here
(http://neuromorpho.org/neuroMorpho/SomaFormat.html)for more
details about the soma format change.
 Neurolucida files that represent soma as a 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 represent 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 default specificity
condition, which is type > -1, (i.e.) all the functions are
applicable to all the arbors of the tree by default. Any
specific conditions can be selected in the specificity panel
for desired function(s). See the related FAQ:
http://cng.gmu.edu:8080/Lm/FAQ/install.html#LM3.8_6
 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

Minor changes:
  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, it returns 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.

Bug Fixes for L-Measure v3.8

 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 6.6 related
to this. The comments printed in the SWC converted files had
extra empty lines in some cases. This has been fixed.
 The SWC conversion of the files that had 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 the Linux version sometimes multiple files would not get

converted at once. 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:
http://cng.gmu.edu:8080/Lm/help/index.htm) to return stems
(different types) only near the soma area.

New Functionalities for 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.
 Added a new “remove all” button in LMSearch panel. This
button will remove all the files from the input file
selection window.

Bug fixes for 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.

FAQ for GUI v4.4

 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?