1. How do I install LM standalone version?
Ans. On the home page there are two downloadable archives for installing LM, choose the appropriate one corresponding to your operating system (Linux or Windows). The extract the Lm.zip on your local machine.
2. I am not able to run the stand alone version of Lm.exe or Lmeasure from the local drive?
Ans. For stand alone version to run smoothly ensure that you have the latest version of Java Virtual Machine. Once you have installed the latest version you can run Lm.exe in the command prompt using the command
On the command prompt, cd (directory where Lm.zip in installed) java -jar Lm.jar
3. How do I run the online version of L-Measure?
Ans. To run the online version you have to click the hyperlink online version on the top of the webpage.
4. What does the different panels do in Lmeasure?
Ans.
5. How can I see LM executable version on a stand alone version?
Ans. After Downloading the Lm.zip, open the java file "Lm.jar".6. What does add do in the specificity panel?
Ans. 'Add->' button is used to select the desired morphological function from the list.
7. What are Connector, Function_name, Operator and value in the specificity panel?
Ans. If you plan to add some more specificity conditions then the file you have added the n connector allows you to choose between 'And' and 'Or'.
Similarly the Operator column allows the user to select b/w '<', '>' and '='.
Value column is a text field which allows you to enter any decimal/integer value.
8. What is the importance of 'Remove' and 'Remove All' in the specifictity panel?
Ans. 'Remove' allows you to delete selected functions from the text area. 'Remove All' allows you to remove all the function in the text area
9. When can we use the Average function?
Ans. Average function is used to find the average of the scatter distribution data with each bin.
10. When can we use the PCA function?
Principal Component Analysis (PCA) will shift the origin to (0,0,0) and rotate the neuron along the long axis. The PCA conversion will therefore shift and rotate the neuron which will relatively affect the width, height and depth measurements from the original orientation. This PCA implementation has been tested on dentate gyrus granule neurons to orient them on perpendicular axis to the granule cell layer.
11. When can we use the XYZ function?
Ans. XYZ (independent of the selected functions) returned a list of 3D coordinates of all compartments that satisfy the Specificity conditions.
12. When do we need 'number of bins' and 'width bins'?
Ans. When we are plotting the scatter distribution data one can have the range for the data according to there needs, by default Lmeasure takes it as 10. If we select 'number of bins' then it computes the range of values of the selected function and uniformly distribute. In 'number of bins' it takes the sum of all the data within the bin. In 'width bins' it takes the average of all the data within the bin.
13. What is the importance of 'Stat_Tests'?
Ans. In the function panel, Select the check box 'Stat_Tests' just beside the list window. This will change the display area on the right to table window with 6 columns namely "function_name", "Sum","Min","Avg","Max" and"SD".
14. What are the formats supported by Lmeasure?
Ans. The input file supported are SWC format, neurolucida format, Amral format, Burke Format, Claiborne Format, Eutectic format.
15. What is the importance of Stat_Tests in input panel?
Ans. The importance of Stat_Tests is initially by clicking the check box Group2 window will be activated. Then by clicking on "Add->" buttons of the Group1 and Group2 respectively one can add neuron files to the Group1 and Group2 windows. The 'Remove' and 'RemoveAll' buttons will remove the selected files from the respective windows. Then choose the stat test to be performed. By default "Wilcoxon test" is selected with no corrections. But you can choose the desired correction and test by selecting from the radio buttons and check boxes.
16. What does Global function perform?
Ans, Global check box allows the user to perform group study. All neuron inserted in the Input panel will be considered as a single structure.
17. What does RAW Data function perform?
Ans. Raw Data check box is marked, data are returned as the extensive list of values from which all statistics are computed. It is recommended to only check this option when a simple function is selected.
18. What does SWC Conversion function perform?
Ans. SWC Conversion check box is marked, a copy of all neurons loaded in the Input panel is converted to SWC format and saved in the same directory of the original files (with the extension .swc added to their original names).
19. What does Subtrees Group function perform?
Ans. Subtrees group check box can be marked to generate the sub trees or analyze the generated sub trees. The sub trees will be generated in SWC format. 1. If 'Generate Subtrees' option is selected, the sub trees of the input neuron is created in 'sub_trees_dir' folder in the same location as the input neuron file. 2. If 'Analyse Subtrees' is selected, only sub trees information is displayed in the Go panel. No sub trees are stored in physical location.
Ans. When we don't want to save to output on the physical location then we can use Go Panel. It will give you the output of the computations that are passed from input panel and display the result in the Go panel.
21. When can we use LMSearch Panel?
Ans. LMSearch is used to search the selected statistical function.
22. How can I load two groups at one time?
Ans. 'Load to group2' button is used to load two groups at one time.
23. How can we run PCA from command line ?
For printing the SWC file after Principal Component Analysis (PCA) use this windows executable and give the following command Lm.exe -C -p /path/to/xyz.swc to generate the PCA converted SWC file, which is saved to the same location as the original file. Please note if there is space in the file path replace it with '+'
For printing the SWC file after Principal Component Analysis (PCA) use this Linux executable and give the following command lmeasure -C -p /path/to/xyz.swc to generate the PCA converted SWC file, which is saved to the same location as the original file. Please note if there is space in the file path replace it with '+'
1. What format of SWC files are accepted as valid input?
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.
1. How can we find the execution time of L-Measure?
err.txt generated by standalone L-Measure gives the timestamp after execution of each neuron. Difference of the time stamps is the execution time of each neuron.
2. How are sub trees processed and saved on the local hard drive?
Generated sub trees are processed based on N_stems. Further, they are sub categorized and saved onto local hard drive based upon their type tags (2=Axon, 3=Basal, 4=Apical).
In response to ongoing discussion in the research community (The NEURON Forum), L-Measure is updating the soma format in the swc conversions of the standardized reconstruction files. As of v3.7.2, all NeuroMorpho.Org somata previously represented as a single point (a 'sphere') will be represented by three 3D points describing a cylinder. This update minimizes confusion and maximizes compatibility with other resources. The conversion was agreed upon and coordinated with the developers of NEURON, L-Measure, and NeuroML. For more details refer to link.
Multiple contours are transformed into a three-point soma. However, for each contour, the center coordinates and radius (xs, ys, zs, rs) are computed as average point of all the circumference points of that contour. Therefore, n soma contours will create (n-1) cylinders. For more details refer to link.
This is expected when the input file has only one soma point, because LM v3.8 converts single soma assumption to cylindrical soma assumption by adding two more points. Hence soma is represented as at least two compartments. Refer to link for more detail.
6. I am getting N_branch and is not same as N_bifs + N_tips
The formula N_branch = N_bifs+N_tips will hold true for analysis with specificity type > 1. Otherwise, since the soma (root) can be more than one point it will give a slightly larger number.
7. Why I am getting 0.5um as diameter for the Amira to SWC conversion?
The default diameter for Amira to SWC conversion is 0.5. We can add parameter dx.xx to the parameters where x.xx is the diameter.
8. Which angle is returned in Bif_ampl_local near soma, in case of multiple stems?
In case of multiple stems, the maximum angle between soma and the stems is returned.
9. What is the maximum number of files which can be used in online L-Measure?
To obtain results in <1.5 mins, it is recommended to use a max. of 10MB. However, the online request can take upto ~60MB files, which takes much longer execution time ~(10 Min).
10. The online L-Measure is not initializing in Linux based OS browsers?
One of the probable reasons is Java is not enabled on the browsers. Follow the steps to enable java on Ubuntu on firefox, similarly it could be done on other combinations of linux based OS and browsers.
Step1 – Install jre 7 •Download the 32bit or 64bit Linux "compressed binary file" - it has a ".tar.gz" file extension. •Uncompress it tar -xvf jre-7-linux-i586.tar.gz •Now run sudo update-alternatives --config java You will get output as: $sudo update-alternatives –config java There are 2 choices for the alternative java (providing /usr/bin/java). Selection Path Priority Status ———————————————————— * 0 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 auto mode 1 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 manual mode 2 /usr/lib/jvm/java-6-sun/jre/bin/java 63 manual mode ------------------------------------------------------------------------------ Press enter to keep the current choice[*], or type selection number: Remember the last number and press enter to exit this utility i.e. in this example remember the number 2. if only one alternative is shown then remember the number 0 •Now run sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jre1.7.0/bin/java 3 This will add your new JRE 7 installation into alternatives list i.e. use the remembered number + 1 i.e. 3 in the example above. - Run sudo update-alternatives --config java You will see output similar one below - choose the number of jre1.7.0 i.e. 3: $sudo update-alternatives –config java There are 3 choices for the alternative java (providing /usr/bin/java). Selection Path Priority Status ———————————————————— * 0 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 auto mode 1 /usr/lib/jvm/java-6-openjdk/jre/bin/java 1061 manual mode 2 /usr/lib/jvm/java-6-sun/jre/bin/java 63 manual mode 3 /usr/lib/jvm/jre1.7.0/jre/bin/java 3 manual mode -------------------------------------------------------------------------------------------- Press enter to keep the current choice[*], or type selection number: 3 update-alternatives: using /usr/lib/jvm/jre1.7.0/jre/bin/java to provide /usr/bin/java (java) in manual mode. N.B. if there was no previous java installation then the new JRE will be the default and you will not see the above. •Check the version of you new JRE 7 installation: java -version ---------------------------------------------------------- java version “1.7.0” Java(TM) SE Runtime Environment (build 1.7.0-b147) Java HotSpot(TM) Client VM (build 21.0-b17, mixed mode) ----------------------------------------------------------- Step2 – Install Firefox/Chrome plugin •mkdir ~/.mozilla/plugins •Remove a former version of the Java plugin (may or may not be present) rm ~/.mozilla/plugins/libnpjp2.so •Now you can install the plugin, by creating a symbolic link (you tell Firefox, where the plugin is located). ln -s /usr/lib/jvm/jre1.7.0/lib/i386/libnpjp2.so ~/.mozilla/plugins/ •Confirm that the JRE has been successful by using the official oracle website.
1. Which compartment types are accepted by L-Measure ?
L-Measure accepts any no. of types (>= 1) as defined in the input reconstruction files. We recommend, not use "0" as type values. However, the standard notation, which most of the SWC files follow is 1 <= type <=4. Please refer to the type function in the help for more detailed explanation.
2. What happens when there is no Soma in the input file?
LM accepts files with no soma for analysis/conversion. Usually axonal reconstructions are the ones that have no soma.
3. Why do I see negative value for taper?
If there are negative values that means the given reconstruction file has smaller parent diameters when compared to the daughter branches.
4. Is SWC file with more than one soma compartment accepted by L-Measure?
Yes, SWC files with multiple soma compartments are accepted. But all the soma compartments (type = 1) must be connected to each other adjacently.
LM skips or discards such bifurcation points where the parent and daughter diameters are the same.
6. Why is PCA conversion crashing?
L-Measure requires at least one soma point to do PCA.
7. Does Taper_1 consider terminal segments?
Yes, Taper_1 is computed on terminal segment.
8. How can we verify the result of N_Branch?
N_Branch = N_Bifs + N_Tips.
1. In which scenario there will no SubTree generation?
If the number of Stems = 0, then there will be no subtree generation.
2. How can we use Subtree Analysis option from command prompt ?
The Subtree analysis option can only be exercised using LM GUI
3. How many significant digits are used after the decimal for XYZ values in SWC conversion?
The values are rounded to 2 decimal digits.
4. How many lines of comments are accepted in any input file used for SWC conversion?
Now any Input file can accept any number of comment lines.
5. How is Fractal Dim computed?
Fractal Dim is computed using the formula Slope(b) = (NSXY - (SX)(SY)) / (NSX2 - (SX)2). For more details see the help docs.