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imported code from https://github.com/wachtlerlab/Reg-MaxS v1.1

Ajayrama Kumaraswamy 1 year ago
parent
commit
c5fcd4aa0b
100 changed files with 66656 additions and 0 deletions
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      .gitignore
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      LICENSE-CCBY
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      ParFiles/PCABased/HSNL.json
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      ParFiles/PCABased/HSNR.json
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      ParFiles/PCABased/HSNR1-4.json
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      ParFiles/PCABased/LLC.json
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      ParFiles/Reg-MaxS-N/HSNL-HSNR.json
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      ParFiles/Reg-MaxS-N/HSNL.json
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      ParFiles/Reg-MaxS-N/LLC.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandRot0.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandRot1.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandScale0.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandTrans0-9.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandTrans1.json
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      ParFiles/Reg-MaxS/HSN-fluoro01.CNGRandTranslate0.json
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      Readme.md
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      TestFiles/HSN-fluoro01.CNG.swc
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      TestFiles/HSN-fluoro01.CNGNoiseStd1.swc
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      TestFiles/HSN-fluoro01.CNGRandTranslate0.swc
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      TestFiles/HSNL/HSN-fluoro02.CNG.swc
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      TestFiles/HSNL/HSN-fluoro03.CNG.swc
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      TestFiles/HSNL/HSN-fluoro06.CNG.swc
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      TestFiles/HSNL/HSN-fluoro08.CNG.swc
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      TestFiles/HSNR/HSN-fluoro01.CNG.swc
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      TestFiles/HSNR/HSN-fluoro05.CNG.swc
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      TestFiles/HSNR/HSN-fluoro07.CNG.swc
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      TestFiles/HSNR/HSN-fluoro09.CNG.swc
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      TestFiles/LLC/Cha-F-000012.CNG.swc
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      TestFiles/LLC/Cha-F-000018.CNG.swc
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      TestFiles/LLC/Cha-F-300051.CNG.swc
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      TestFiles/LLC/Cha-F-300331.CNG.swc
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      TestFiles/LLC/Cha-F-400051.CNG.swc
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      TestFiles/LLC/Cha-F-400051.CNG/Cha-F-400051.CNG.swc
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      TestFiles/LLC/Gad1-F-000062.CNG.swc
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      TestFiles/LLC/Gad1-F-600000.CNG.swc
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      regmaxsn/__init__.py
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      regmaxsn/core/RegMaxSPars.py
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      regmaxsn/core/SWCTransforms.py
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      regmaxsn/core/__init__.py
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      regmaxsn/core/farthestPointStats.py
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      regmaxsn/core/iterativeRegistration.py
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      regmaxsn/core/matplotlibRCParams.py
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      regmaxsn/core/maxDistanceBasedMetric.py
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      regmaxsn/core/misc.py
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      regmaxsn/core/occupancyBasedMeasure.py
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      regmaxsn/core/plotDensities.py
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      regmaxsn/core/rotOnce.py
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      regmaxsn/core/scaleOnce.py
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      regmaxsn/core/swcFuncs.py
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      regmaxsn/core/transOnce.py
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      regmaxsn/core/transforms.py

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.gitignore

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+*.iml
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+tmp
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+*egg-info
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LICENSE-CCBY

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ParFiles/PCABased/HSNL.json

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+[{"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNL/HSN-fluoro02.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro03.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNL/HSN-fluoro03.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro06.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNL/HSN-fluoro06.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro08.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNL/HSN-fluoro08.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro02.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNL/HSN-fluoro10.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNL/HSN-fluoro10.CNG.swc"}]

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ParFiles/PCABased/HSNR.json

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+[{"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro01.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro04.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro04.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro05.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro05.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro07.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro07.CNG.swc"}, {"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro09.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro09.CNG.swc"}]

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ParFiles/PCABased/HSNR1-4.json

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+[{"usePartsDir": false, "refSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro01.CNG.swc", "gridSizes": [40.0, 20.0, 10.0], "testSWC": "/home/aj/repos/Reg-MaxS/TestFiles/HSNR/HSN-fluoro04.CNG.swc", "resFile": "/home/aj/repos/Reg-MaxS/Results/PCABased/HSNR/HSN-fluoro04.CNG.swc"}]

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ParFiles/PCABased/LLC.json

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Readme.md

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+Welcome to regmaxsn repository!
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+
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+Description
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+---
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+
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+**Reg-MaxS and Reg-MaxS-N: Algorithms for co-registration of pairs and groups of neuron morphologies based on maximization of spatial overlap**
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+
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+These algorithms have been discussed in detail in the following publication:
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+
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+Kumaraswamy A., Kai K., Ai H., Ikeno H., Wachtler T. (2018). "Spatial registration of neuron morphologies based on maximization of volume overlap". In *BMC Bioinformatics*, DOI: [10.1186/s12859-018-2136-z](https://doi.org/10.1186/s12859-018-2136-z)
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+
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+This repository contains scripts for running Reg-MaxS and Reg-MaxS-N algorithms for registering pairs and groups of neuron morphologies respectively.
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+
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+The algorithms are written in  Python and at the moment work only with SWC files.
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+
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+# Installation
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+
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+
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+With Conda (Linux or Windows):
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+
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+1. Create a new environment: 
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+>conda create --name regmaxsn python=2.7 numpy scipy pillow matplotlib scikit-learn pandas seaborn openpyxl xlrd statsmodels
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+2. Activate environment: 
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+>(on Linux) source activate regmaxsn 
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+>(on Windows) activate regmaxsn
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+3. Install regmaxsn: 
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+>pip install \<path to Reg-MaxS repository\>
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+4. Create Reg-MaxS Workspace. Note where your Reg-MaxS Workspace is created.
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+>python \<path to Reg-MaxS repository\>/setupWorkspace.py
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+
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+Without Conda, with pip and virtualenvwrapper (only for Linux):
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+
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+1. Create a new environment: 
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+>mkvirtualenv regmaxsn
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+2. Activate environment: 
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+>workon regmaxsn
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+3. Install regmaxsn:
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+>pip install \<path to Reg-MaxS repository\>
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+4. Create Reg-MaxS Workspace. Note where your Reg-MaxS Workspace is created.
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+>python \<path to Reg-MaxS repository\>/setupWorkspace.py
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+
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+NOTE: This environment must be activated every time you want to run Reg-MaxS, Reg-MaxS-N or any other scripts of this package.
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+
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+# Usage:
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+
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+## Reg-MaxS
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+
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+1. First you need to create a parameter file for Reg-MaxS. This is created using the file
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+> \<path to your Reg-MaxS Workspace\>/utilityScripts/constructRegMaxSParFile.py
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+
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+You need to open this .py file in a editor and change variables as needed. The detailed usage instructions of this script are provided at the top of it. Two different use cases have been illustrated using three examples. Take a look at them and modify the script according to your needs.
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+
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+2. After editing the "constructRegMaxSParFile.py" as needed, create a parameter file as below:
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+> python \<path to your Reg-MaxS Workspace\>/utilityScripts/constructRegMaxSParFile.py
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+
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+3. Run Reg-MaxS with this parameter file:
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+> python -m regmaxsn.scripts.algorithms.RegMaxS \<path to the above created Reg-MaxS parameter file\>
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+
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+## Reg-MaxS-N
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+
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+1. First you need to create a parameter file for Reg-MaxS-N. This is created using the file
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+> \<path to your Reg-MaxS Workspace\>/utilityScripts/constructRegMaxSNParFile.py
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+
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+You need to open this .py file in a editor and change variables as needed. The detailed usage instructions of this script are provided at the top of it. Two different use cases have been illustrated using three examples. Take a look at them and modify the script according to your needs.
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+
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+2. After editing the "constructRegMaxSNParFile.py" as needed, create a parameter file as below:
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+> python \<path to your Reg-MaxS Workspace\>/utilityScripts/constructRegMaxSNParFile.py
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+
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+3. Run Reg-MaxS-N with this parameter file:
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+> python -m regmaxsn.scripts.algorithms.RegMaxSN \<path to the above created Reg-MaxS-N parameter file\>

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TestFiles/HSNR/HSN-fluoro04.CNG.swc

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1
+# SWC to SWC conversion from L-Measure. Sridevi Polavaram: spolavar@gmu.edu
2
+# Original fileName:/cng_repository/Soumya/LM_Automated_Testing_Enviornment/Test_Lm3.7.2_11022011_SG_Linux_NMOConv8/TestResults/LoadTest/test_52/HSN-fluoro04.CNG.swc
3
+#
4
+# Original file HSN-fluoro04.swc edited using StdSwc version 1.31 on 5/31/11.
5
+# Irregularities and fixes documented in HSN-fluoro04.swc.std.  See StdSwc1.31.doc for more information.
6
+#
7
+# HSN neuron (lobula place tangential cells, LPTC) from Calliphora vicina
8
+# identification by response properties, in vivo Alexa injection, 2-photon-microscopy imaging, x63 objective, multiple image tiles
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+# reconstructed and processed with Matlab and the TREES toolbox http://www.treestoolbox.org
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+# scaling 1:1:1 um
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+#  Max Planck Institute of Neurobiology, Martinsried, Germany
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+#  Systems and Computational Neuroscience, Alexander Borst
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+#  published in "The morphological identity of insect dendrites" Cuntz H, Forstner F, Haag J, Borst A. PMID 19112481
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File diff suppressed because it is too large
+ 1917 - 0
TestFiles/HSNR/HSN-fluoro05.CNG.swc


+ 931 - 0
TestFiles/HSNR/HSN-fluoro07.CNG.swc

@@ -0,0 +1,931 @@
1
+# SWC to SWC conversion from L-Measure. Sridevi Polavaram: spolavar@gmu.edu
2
+# Original fileName:/cng_repository/Soumya/LM_Automated_Testing_Enviornment/Test_Lm3.7.2_11022011_SG_Linux_NMOConv8/TestResults/LoadTest/test_52/HSN-fluoro07.CNG.swc
3
+#
4
+# Original file HSN-fluoro07.swc edited using StdSwc version 1.31 on 5/31/11.
5
+# Irregularities and fixes documented in HSN-fluoro07.swc.std.  See StdSwc1.31.doc for more information.
6
+#
7
+# HSN neuron (lobula place tangential cells, LPTC) from Calliphora vicina
8
+# identification by response properties, in vivo Alexa injection, 2-photon-microscopy imaging, x63 objective, multiple image tiles
9
+# reconstructed and processed with Matlab and the TREES toolbox http://www.treestoolbox.org
10
+# scaling 1:1:1 um
11
+#  Max Planck Institute of Neurobiology, Martinsried, Germany
12
+#  Systems and Computational Neuroscience, Alexander Borst
13
+#  published in "The morphological identity of insect dendrites" Cuntz H, Forstner F, Haag J, Borst A. PMID 19112481
14
+# SCALE 1.0 1.0 1.0 
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