1.2.0 version (#15)

* firstpass tutorial

* generalizing the kcsd for the tutorial

* updates to the ipython notebook

* missing file

* 2d version tutorial 90% done

* working 2d and 60% 3d cases

* 3D case now inc.

* adding some buttons

* finalizing the details

* adding additonal variables for the kcsd

* fixing default params

* making tutorials work with the new folder strut

* adding missing files and imports

* fixing xrange problem

* fixing dict problem

* setuptools compatible and installation friendly in prep for ttd

* towards tests

* first pass travis

* testing travis

* travisblues

* removing matplotlib dep

* refinements

* getting the figure right this time;

* badge image

* fixing builds

* coveralls test

* fixing dependency

* test

* here we go again

* increasing coverage

* last time perhspas

* moving csd test functions

* updating readme

* binder, automatic ipython notebooks

* testing binder

* binder fix in yml config

* trying to display widgets by default

* postbuild should be executable

* missing default parameter h in KCSD3D (#10)

* consistent electrode markers

* missing default parameter h in KCSD3D

* build the prs on branch

* Error maps (#12)

* code moved to Python 3 (with Python 2 compatibility)

* diagnostic tools for kCSD method

* plots of singular vectors changes

* plots for kCSD3D

* including updated kCSD core library

* consistent electrode markers

* validation classes compatible with git version of KCSD code

* removed old separate files for kCSD method, consistent electrodes markers

* broken electrodes for 1D and 3D, added docstrings

* validation class created

* removed tests folder

* removed saving commands

* error maps in tutorial

* removed unused files

* moved files to new directory

* missing default parameter in KCSD3D

* missing default parameter h in KCSD3D

* files merged from upstream

* consistent documentation

* merged from ipynb_tests

* importing compatible with kcsd package

* tutorial including kcsd package, validation classes and error maps

* removed old version of tutorial's files

* method plot_mean_error changed to plot_error_map

* parameters of crossvalidation in make_reconstruction method

* uppercase global names

* common generate_csd method for all dimensions

* tutorial with error maps - first version

* added the authorship

* handling exceptions

* changed names of validation classes

* investigating relationship between singular values and values of lambda

* remove generate.py

* ValidateKCSD.. and ErrorMap.. classes available directly from kcsd module

* 'binder' pointers to kcsd_tutorial.ipynb

* changed structure of generate_electrodes method

* changed plotting options in tutorial, refactored main code

* error_map renamed to visibility_map

* fixing some merge related issues

* L-curve upgrade

* xx

* Fater implementation of the L-curve

* L-curve upgrade

* ..

* Revert 13 ipynb tests (#16)

* Revert ".."

This reverts commit e17f83d.

* Revert "L-curve upgrade"

This reverts commit 3ddd1b4.

* Revert "Fater implementation of the L-curve"

This reverts commit 2ce0512.

* Revert "xx"

This reverts commit e2ef67f.

* Revert "L-curve upgrade"

This reverts commit a36bdf4.

* Ipynb tests (#18)

* KCSD.py and utility_functions.py. update

* no plots

* Ipynb tests (#22)

* consistent electrode markers

* missing default parameter h in KCSD3D

* fixing tests errors

* fixing broken electrodes number

* fixing sKCSD import error

* fixed kcsd tests

* L-curve method included in validation code and tutorial

* moving data to the corresponding folder, and making first start changes to the tests for skcsd

* moving sKCSD stuff around

* removing sklearn dep and n_jobs issues

* restoring tests functionality

* fixes to 1.2.0 (#25)

* consistent electrode markers

* missing default parameter h in KCSD3D

* fixing tests errors

* fixing broken electrodes number

* fixing sKCSD import error

* fixed kcsd tests

* L-curve method included in validation code and tutorial

* modified version of numpy in setup.py

* changed minimal numpy version

* cubic root without numpy.cbrt

* l-curve method for 2D and 3D validation cases

* fixed bug in visibility maps - correct broken ele grid

* Tutorial 3d plus size (#28)

* consistent electrode markers

* missing default parameter h in KCSD3D

* fixing tests errors

* fixing broken electrodes number

* fixing sKCSD import error

* fixed kcsd tests

* L-curve method included in validation code and tutorial

* modified version of numpy in setup.py

* changed minimal numpy version

* cubic root without numpy.cbrt

* l-curve method for 2D and 3D validation cases

* fixed bug in visibility maps - correct broken ele grid

* mlab.griddata changed to scipy.interpolate.griddata

* fixed visibility maps for 3D cases

* reconstruction with Visibility Map mask

* modified noise selection option

* basic validation for MoIKCSD

* corrected docstrings

* Address sKCSD issues (#27)

* sKCSD support for swc morphologies

* Params improvement

* Small test

* Ploting function for skCSD results, 2D morphology plot improved

* Comment added

* Loader, saver for simulation

* Fix slashes in paths

* Make Python2 and Python3 compatible

* Empty __init__ file

* Add untracked directories

* Tutorial data

* Comments on morphology and electrode positions data format

* Ignore *~ and #*

* Object loading and storing data for sKCSD3D

* Find paths of the morphology, LFP and electrode positions files

* Data for tests

* Test loading morphology

* Load electrode positions

* Load data

* Ball and stick model with 8 electrodes

* Ball and stick model with 16 electrodes

* Ball and stick model with 128 electrodes

* Correct morphology

* Use data loder

* Correct morphology

* Store preprocessed data in data directory

* Correct axes labels in morphology plots

* Fix paths in sKCD3D example

* Add extent

* Calculate kernels for ball and stick

* Fix plotting neurons

* Change pickle to json

* Script for running simulations and different morphologies

* Ignore backup files while loading files for sKCSD

* Fix paths

* Choose which electrode to plot

* Script for generating fig 2

* Load only swc files

* Remove unnecessary prints

* Loop over electrode number

* Save membrane current

* Add tstop

* Fix elctrode distance bug

* Bug fix -- last segment does have a parent

* Loop back using parent information

* Fix setting correct electrode positions

* Make figure

* Wider range for morphology

* Use parent section information to build swc tree

* Fix scaling in sKCSD3D example

* Test if all the sources are distributed within the cell

* Save ids of dendrites connected while enclosing morphology

* Change width of gauss and source number in example

* Fix comparing paths in loadData test

* Add checking if all branches are covered with loops

* Test data

* Ignore pngs

* Test kCSD calculation for ball and stick

* Save loops as an array

* Try out more points in fig 2

* Fix imports and paths

* More interpolation points for potential estimation for skCSD

* Implement KCSD calculation using points on the 1D morphology for estimation.

cell_pos, which stores dendrite locations on the morphology loop, was added to sKCSDcell.
B tilda uses distance between sources and dendrites on the morphology loop now.
B uses distance between source positions (x,y,z) and electrode positions now.
Add transformation of CSD which is calculated on the morphology loop to cartesian coordinates.
Basis was switch to 1D.
The grid parameters are no longer necessary.

* Sinusoid synaptic stimulation for fig 1

* Remove unnecessary parameters

* Dendritic segment cannot be smaller than 2 um for CSD and potential transformation

* Remove unnecessary grid parameters from example of sKCSD reconstruction

* First version of the code

* Change output filenames

* Cosine synaptic stimulation with frequency dependent on segment location

* CSD calculation as default

* Code refactoring

* Save potential and current on 1D morphology and 3D grid

* Move csd transformation from sKCSD3D to sKCSDcell

* Hoc file to generate y-shaped neuron

* Fix bug in finding parent

* Code refactorization for csd and potential calculation in 3D

* Symmetric stimulation of a Y-shaped neuron

* First version of Fig 3

* Random grid

* Fig 4 of eLife article

* Change script names to match figure numbers in the published article

* Change get to pop to notify user if he used nonexistent key arguments

* Make one figure

* Create separate directory for figures

* Fix typo

* Move most common sequences of operations to module functions

* Fig 7

* Domi electrodes

* Correct Domi path

* Correct L1 error calculation

* Make compatible with new LFPy

* Small branched morphology for tests

* Account for branches longer than shorterst branch

* Add small non-trivial neuron morphology to test transformation to 3D

* Add extent argument to plotting with imshow

* Remove looping over R and lambda. Clean up the code

* Remove unused code

* Return cell object after simulations not just the directory

* Hex grid and injection of oscillatory current with random synaptic stimulation

* Set dt

* Correct potential calculation

Intergrate over s from -2R to morphology loop length +2R of source divided by position (Eq 17).

* .5 ms simulation dt

* Add hexagonal grid parameter to keyword arguments of simulation functions

* A more reasonable default R

* Print path when saving csd

* Fix order in oscillatory stimulation

* Default grain of the 3D grid 2e-6

* Add more buttons

* Use classmethod setupClass instead of setUp function

* Clean up code to reflect changes in sKCSD3D

* Assure absolute imports (Python3 compatibility)

* Python 3 compatibility -- absolute imports

* Add changing dt

* Take into account point 0 of the morphology

* Add option of returning CSD/potential in the loop space

* Add test checking 1D loop  to 3D cartesian interpolation

* Specify the initial point at the beginning of the morphology file

* Loop over possible R and lambda values

Transform Dori's lambda values to kCSD lambda values: in kCSD Gaussian functions are normalized (divided) by (2*pi)^0.5*R, kernels are normalized by number of sources and potentials are divided by 4*pi*sigma.

* Add interpolation tests for the larger cell

* Add interpolation tests for the larger cell

* Simplify placing sources

Fist loop around morphology (same algorythm as before, without placing sources). Place sources on the morphology. Find source cartesian coordinates using interpolation and loop coordinates, both on the morphology loop and in 3D.

* Fix import and typo

* Fix saving 3D morphology

* Remove unused variables

* Add max_dist tests

* Further tests for total length of the morphology loop

Check if max_dist calculated during looping over morphology is equall to total distance calculated using the morphology file.

* Add docstrings. Remove unused function

* Add class description

* Add autorship

* Change sKCSD3D class name to sKCSD

* Rename sKCSD3D to sKCSD

* Remove weights

* Works with skmonaco

* Add tests for sKCSDcell.points_in_between()

* Change cell to one used in tutorials

* Divide get_grid to 2 functions

* Y-shaped neuron

* Test finding 3D loop coordinates

* Test continuity

* Remove unnecessary prints

* Add dist_table_density to docstring

* On transformation parameter for sKCSD

'3D' -- transforms quantity (CSD or potential) to 3D
'segments' -- transforms quantity to neuron's segments
None -- no transformation, quantity is in the morphology loop space

* Test, if CSD/potential is the right shape

* Move loop to segment transformation to sKCSDcell object

* Save CSD and potential in loop space

* Fix too many arguments in saving simulations

* Basic version of plotting results in 3D, loop and segment space

* Extent matching 3D properties of the cell

* Move ploting maps to plotting_functions

* Ball and stick data for tests

* import run_LFP after compiling sinsyn.mod

* Move compiling sinsyn.mod before importing LFPy

* Move specifying saving directory to utility functions

* Remove unused buttons

* Linear interpolation on xyz position on the morphology loop

* 1 or 3 column files with electrode positions

* Move loadData to tutorials

* Lower cosine injection

* Add running sKCSD for arbitrary data

Specify path to morphology, electrode positions and LFP. Move loadData to tutorials.

* loadData in tutorials

* Fix lambda range

* Unify units of estimated CSD and ground truth

* Remove unused files

* Merge sKCSD.py and sKCSDcell.py

* Fix path to loadData

* Rename functions.py to sKCSD_utils.py

* Pep8 compatibility

* Pep8 compatibility

* Pep8 compatibility

* Pep8

* Pep8

* Pep8

* Fix paths so test of loadData pass

* Move Bresenham algorithm to functions

* Remove obsolete tests

* Correct numpy version

* Fix bug in test_ball_and_stick_8

* Lower numpy version

* Change numpy and scipy versions for min_conda to pass tests

* Move sKCSD_paper to figures/sKCSD_paper (#29)

* sKCSD support for swc morphologies

* Params improvement

* Small test

* Ploting function for skCSD results, 2D morphology plot improved

* Comment added

* Loader, saver for simulation

* Fix slashes in paths

* Make Python2 and Python3 compatible

* Empty __init__ file

* Add untracked directories

* Tutorial data

* Comments on morphology and electrode positions data format

* Ignore *~ and #*

* Object loading and storing data for sKCSD3D

* Find paths of the morphology, LFP and electrode positions files

* Data for tests

* Test loading morphology

* Load electrode positions

* Load data

* Ball and stick model with 8 electrodes

* Ball and stick model with 16 electrodes

* Ball and stick model with 128 electrodes

* Correct morphology

* Use data loder

* Correct morphology

* Store preprocessed data in data directory

* Correct axes labels in morphology plots

* Fix paths in sKCD3D example

* Add extent

* Calculate kernels for ball and stick

* Fix plotting neurons

* Change pickle to json

* Script for running simulations and different morphologies

* Ignore backup files while loading files for sKCSD

* Fix paths

* Choose which electrode to plot

* Script for generating fig 2

* Load only swc files

* Remove unnecessary prints

* Loop over electrode number

* Save membrane current

* Add tstop

* Fix elctrode distance bug

* Bug fix -- last segment does have a parent

* Loop back using parent information

* Fix setting correct electrode positions

* Make figure

* Wider range for morphology

* Use parent section information to build swc tree

* Fix scaling in sKCSD3D example

* Test if all the sources are distributed within the cell

* Save ids of dendrites connected while enclosing morphology

* Change width of gauss and source number in example

* Fix comparing paths in loadData test

* Add checking if all branches are covered with loops

* Test data

* Ignore pngs

* Test kCSD calculation for ball and stick

* Save loops as an array

* Try out more points in fig 2

* Fix imports and paths

* More interpolation points for potential estimation for skCSD

* Implement KCSD calculation using points on the 1D morphology for estimation.

cell_pos, which stores dendrite locations on the morphology loop, was added to sKCSDcell.
B tilda uses distance between sources and dendrites on the morphology loop now.
B uses distance between source positions (x,y,z) and electrode positions now.
Add transformation of CSD which is calculated on the morphology loop to cartesian coordinates.
Basis was switch to 1D.
The grid parameters are no longer necessary.

* Sinusoid synaptic stimulation for fig 1

* Remove unnecessary parameters

* Dendritic segment cannot be smaller than 2 um for CSD and potential transformation

* Remove unnecessary grid parameters from example of sKCSD reconstruction

* First version of the code

* Change output filenames

* Cosine synaptic stimulation with frequency dependent on segment location

* CSD calculation as default

* Code refactoring

* Save potential and current on 1D morphology and 3D grid

* Move csd transformation from sKCSD3D to sKCSDcell

* Hoc file to generate y-shaped neuron

* Fix bug in finding parent

* Code refactorization for csd and potential calculation in 3D

* Symmetric stimulation of a Y-shaped neuron

* First version of Fig 3

* Random grid

* Fig 4 of eLife article

* Change script names to match figure numbers in the published article

* Change get to pop to notify user if he used nonexistent key arguments

* Make one figure

* Create separate directory for figures

* Fix typo

* Move most common sequences of operations to module functions

* Fig 7

* Domi electrodes

* Correct Domi path

* Correct L1 error calculation

* Make compatible with new LFPy

* Small branched morphology for tests

* Account for branches longer than shorterst branch

* Add small non-trivial neuron morphology to test transformation to 3D

* Add extent argument to plotting with imshow

* Remove looping over R and lambda. Clean up the code

* Remove unused code

* Return cell object after simulations not just the directory

* Hex grid and injection of oscillatory current with random synaptic stimulation

* Set dt

* Correct potential calculation

Intergrate over s from -2R to morphology loop length +2R of source divided by position (Eq 17).

* .5 ms simulation dt

* Add hexagonal grid parameter to keyword arguments of simulation functions

* A more reasonable default R

* Print path when saving csd

* Fix order in oscillatory stimulation

* Default grain of the 3D grid 2e-6

* Add more buttons

* Use classmethod setupClass instead of setUp function

* Clean up code to reflect changes in sKCSD3D

* Assure absolute imports (Python3 compatibility)

* Python 3 compatibility -- absolute imports

* Add changing dt

* Take into account point 0 of the morphology

* Add option of returning CSD/potential in the loop space

* Add test checking 1D loop  to 3D cartesian interpolation

* Specify the initial point at the beginning of the morphology file

* Loop over possible R and lambda values

Transform Dori's lambda values to kCSD lambda values: in kCSD Gaussian functions are normalized (divided) by (2*pi)^0.5*R, kernels are normalized by number of sources and potentials are divided by 4*pi*sigma.

* Add interpolation tests for the larger cell

* Add interpolation tests for the larger cell

* Simplify placing sources

Fist loop around morphology (same algorythm as before, without placing sources). Place sources on the morphology. Find source cartesian coordinates using interpolation and loop coordinates, both on the morphology loop and in 3D.

* Fix import and typo

* Fix saving 3D morphology

* Remove unused variables

* Add max_dist tests

* Further tests for total length of the morphology loop

Check if max_dist calculated during looping over morphology is equall to total distance calculated using the morphology file.

* Add docstrings. Remove unused function

* Add class description

* Add autorship

* Change sKCSD3D class name to sKCSD

* Rename sKCSD3D to sKCSD

* Remove weights

* Works with skmonaco

* Add tests for sKCSDcell.points_in_between()

* Change cell to one used in tutorials

* Divide get_grid to 2 functions

* Y-shaped neuron

* Test finding 3D loop coordinates

* Test continuity

* Remove unnecessary prints

* Add dist_table_density to docstring

* On transformation parameter for sKCSD

'3D' -- transforms quantity (CSD or potential) to 3D
'segments' -- transforms quantity to neuron's segments
None -- no transformation, quantity is in the morphology loop space

* Test, if CSD/potential is the right shape

* Move loop to segment transformation to sKCSDcell object

* Save CSD and potential in loop space

* Fix too many arguments in saving simulations

* Basic version of plotting results in 3D, loop and segment space

* Extent matching 3D properties of the cell

* Move ploting maps to plotting_functions

* Ball and stick data for tests

* import run_LFP after compiling sinsyn.mod

* Move compiling sinsyn.mod before importing LFPy

* Move specifying saving directory to utility functions

* Remove unused buttons

* Linear interpolation on xyz position on the morphology loop

* 1 or 3 column files with electrode positions

* Move loadData to tutorials

* Lower cosine injection

* Add running sKCSD for arbitrary data

Specify path to morphology, electrode positions and LFP. Move loadData to tutorials.

* loadData in tutorials

* Fix lambda range

* Unify units of estimated CSD and ground truth

* Remove unused files

* Merge sKCSD.py and sKCSDcell.py

* Fix path to loadData

* Rename functions.py to sKCSD_utils.py

* Pep8 compatibility

* Pep8 compatibility

* Pep8 compatibility

* Pep8

* Pep8

* Pep8

* Fix paths so test of loadData pass

* Move Bresenham algorithm to functions

* Remove obsolete tests

* Correct numpy version

* Fix bug in test_ball_and_stick_8

* Lower numpy version

* Change numpy and scipy versions for min_conda to pass tests

* Move sKCSD paper files from sKCSD_paper to figure/sKCSD_paper

* Correct LoadData import

* in prep for merger

Author: ccluri

.gitignore

@@ -54,6 +54,9 @@ coverage.xml
 # Django stuff:
 *.log
 
+# coveralls
+/coverage/
+
 # Sphinx documentation
 docs/_build/
 

.travis.yml

@@ -0,0 +1,53 @@
+dist: precise
+language: python
+sudo: false
+python:
+  - 2.7.13
+
+branches:
+  only:
+  - master
+
+env:
+  matrix:
+    # This environment tests the newest supported anaconda env
+    - DISTRIB="conda" PYTHON_VERSION="2.7"
+      NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1"
+      SIX_VERSION="1.10.0" COVERAGE="true"
+    - DISTRIB="conda" PYTHON_VERSION="3.5"
+      NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1"
+      SIX_VERSION="1.10.0" COVERAGE="true"
+
+    # # This environment tests conda extras skmonaco and matplotlib
+    # - DISTRIB="conda_extra" PYTHON_VERSION="3.5"
+    #   NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1"
+    #   SIX_VERSION="1.10.0" COVERAGE="true"
+
+    # This environment tests minimal dependency versions
+    - DISTRIB="conda_min" PYTHON_VERSION="2.7"
+      SIX_VERSION="1.10.0" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1"
+      COVERAGE="true"
+    - DISTRIB="conda_min" PYTHON_VERSION="3.4"
+      SIX_VERSION="1.10.0" NUMPY_VERSION="1.10.4" SCIPY_VERSION="0.16.1"
+      COVERAGE="true"
+
+    # basic Ubuntu build environment
+    - DISTRIB="ubuntu" PYTHON_VERSION="2.7"
+      NUMPY_VERSION="1.8.0" SCIPY_VERSION="0.14.0" SIX_VERSION="1.10.0"
+      COVERAGE="true"
+
+    # - DISTRUB="ubuntu_extra" PYTHON_VERSION="2.7"
+    #   SKMONACO_VERSION="0.2" NUMPY_VERSION="1.13.0" SCIPY_VERSION="1.0.0"
+    #   MATPLOTLIB_VERSION="0.99"  SIX_VERSION="1.10.0" COVERAGE="true"
+
+# Turn off notifications
+notifications:
+  email: false
+
+# command to install dependencies
+install: source continuous_integration/install.sh
+# command to run tests
+script: bash continuous_integration/test_script.sh
+after_success:
+- if [[ "$COVERAGE" == "true" ]]; then coveralls || echo "failed"; fi
+  

AUTHORS.txt

@@ -0,0 +1,8 @@
+include LICENSE.txt
+include README.rst
+graft data
+graft figures
+graft doc
+graft tests
+graft validation
+global-exclude *.py[cod] __pycache__ *.so

LICENSE.txt

@@ -0,0 +1,140 @@
+Kernel Current Source Density
+=============================
+
+This is v1.2 version of kCSD inverse method proposed in
+
+J. Potworowski, W. Jakuczun, S. Łęski, D. K. Wójcik
+"Kernel Current Source Density Method"
+Neural Computation 24 (2012), 541–575
+
+For citation policy see the end of this file.
+
+
+Code status
+-----------
+
+master branch
+
+.. image:: https://travis-ci.org/Neuroinflab/kCSD-python.png?branch=master
+   :target: https://travis-ci.org/Neuroinflab/kCSD-python
+
+.. image:: https://coveralls.io/repos/github/Neuroinflab/kCSD-python/badge.png?branch=master
+   :target: https://coveralls.io/github/Neuroinflab/kCSD-python?branch=master
+
+kcsd library basics (click to open in browser,  jupyter notebook)
+	    
+.. image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_basic.ipynb
+
+kcsd library advanced (click to open in browser,  jupyter notebook)
+
+.. image:: https://mybinder.org/badge.svg
+   :target: https://mybinder.org/v2/gh/Neuroinflab/kCSD-python/master?filepath=tutorials%2Ftutorial_advanced.ipynb
+	    
+Earlier Stable versions
+-----------------------
+Please see git tags for earlier versions
+
+- v1.0 corresponds to the version with the test cases written inside tests folder
+- v1.1 corresponds to the elephant python library version - no tests here
+
+
+License
+-------
+`Modified BSD License`_
+
+.. _Modified BSD License: https://opensource.org/licenses/BSD-3-Clause
+
+
+Installation
+------------
+
+pip install .
+
+or
+
+python setup.py install
+
+(for development / purposes)
+
+pip install -e .
+
+or
+
+python setup.py develop
+
+
+Requirements
+------------
+
+- python 2.7 / 3.4 / 3.5
+- numpy 1.10
+- scipy 0.17
+
+
+Additional Packages
+-------------------
+
+- scikit-monaco 0.2 (for monte carlo type integration for 3D case)
+- matplotlib 0.99 (for visualization and plotting)
+
+
+Status
+------
+
+- KCSD1D 
+- KCSD2D 
+- KCSD3D 
+- MoIKCSD
+- sKCSD
+
+
+Usage
+-----
+
+from kcsd import KCSD1D, KCSD2D, KCSD3D, MoIKCSD, sKCSD
+
+from kcsd import utility_functions as utils
+
+from kcsd import csd_profile as CSD
+
+
+
+For data acquired from experiments, please use Elephant_ instead.
+
+.. _Elephant: http://neuralensemble.org/elephant/
+
+
+Contact
+-------
+Prof. Daniel K. Wojcik
+
+d.wojcik[at]nencki[dot]gov[dot]pl
+
+
+
+Citation policy
+---------------
+If you use this software in published research please cite the following work
+
+- KCSD1D - [1, 2]
+- KCSD2D - [1, 3]
+- KCSD3D - [1, 4]
+- MoIkCSD - [1, 3, 5]
+- sKCSD - [6]
+  
+1) Potworowski, J., Jakuczun, W., Łęski, S. & Wójcik, D. (2012) 'Kernel current source density method.' Neural Comput 24(2), 541-575.
+
+2) Pettersen, K. H., Devor, A., Ulbert, I., Dale, A. M. & Einevoll, G. T. (2006) 'Current-source density estimation based on inversion of electrostatic forward solution: effects of finite extent of neuronal activity and conductivity discontinuities.' J Neurosci Methods 154(1-2), 116-133.
+
+3) Łęski, S., Pettersen, K. H., Tunstall, B., Einevoll, G. T., Gigg, J. & Wójcik, D. K. (2011) 'Inverse Current Source Density method in two dimensions: Inferring neural activation from multielectrode recordings.' Neuroinformatics 9(4), 401-425.
+
+4) Łęski, S., Wójcik, D. K., Tereszczuk, J., Świejkowski, D. A., Kublik, E. & Wróbel, A. (2007) 'Inverse current-source density method in 3D: reconstruction fidelity, boundary effects, and influence of distant sources.' Neuroinformatics 5(4), 207-222.
+
+5) Ness, T. V., Chintaluri, C., Potworowski, J., Łeski, S., Głabska, H., Wójcik, D. K. & Einevoll, G. T. (2015) 'Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs).' Neuroinformatics 13(4), 403-426.
+
+
+6) D. Cserpan, D. Meszena, L. Wittner, K. Toth, I. Ulbert, Z. Somogyvari, D. K. Wójcik (2017) 'Revealing The Distribution Of Transmembrane Currents Along The Dendritic Tree Of A Neuron With Known Morphology From Extracellular Recordings.' eLife (2017) 6:e29384
+
+
+

MANIFEST.in

@@ -0,0 +1,51 @@
+channels:
+  - defaults
+dependencies:
+  - ca-certificates=2017.08.26=h1d4fec5_0
+  - certifi=2018.1.18=py36_0
+  - cycler=0.10.0=py36h93f1223_0
+  - dbus=1.12.2=hc3f9b76_1
+  - expat=2.2.5=he0dffb1_0
+  - fontconfig=2.12.4=h88586e7_1
+  - freetype=2.8=hab7d2ae_1
+  - glib=2.53.6=h5d9569c_2
+  - gst-plugins-base=1.12.4=h33fb286_0
+  - gstreamer=1.12.4=hb53b477_0
+  - icu=58.2=h9c2bf20_1
+  - intel-openmp=2018.0.0=hc7b2577_8
+  - jpeg=9b=h024ee3a_2
+  - libedit=3.1=heed3624_0
+  - libffi=3.2.1=hd88cf55_4
+  - libgcc-ng=7.2.0=h7cc24e2_2
+  - libgfortran-ng=7.2.0=h9f7466a_2
+  - libpng=1.6.34=hb9fc6fc_0
+  - libstdcxx-ng=7.2.0=h7a57d05_2
+  - libxcb=1.12=hcd93eb1_4
+  - libxml2=2.9.7=h26e45fe_0
+  - matplotlib=2.1.2=py36h0e671d2_0
+  - mkl=2018.0.1=h19d6760_4
+  - ncurses=6.0=h9df7e31_2
+  - numpy=1.14.0=py36h3dfced4_1
+  - openssl=1.0.2n=hb7f436b_0
+  - pcre=8.41=hc27e229_1
+  - pip=9.0.1=py36h6c6f9ce_4
+  - pyparsing=2.2.0=py36hee85983_1
+  - pyqt=5.6.0=py36h0386399_5
+  - python=3.6.4=hc3d631a_1
+  - python-dateutil=2.6.1=py36h88d3b88_1
+  - pytz=2018.3=py36_0
+  - qt=5.6.2=hd25b39d_14
+  - readline=7.0=ha6073c6_4
+  - scipy=1.0.0=py36hbf646e7_0
+  - setuptools=38.4.0=py36_0
+  - sip=4.18.1=py36h51ed4ed_2
+  - six=1.11.0=py36h372c433_1
+  - sqlite=3.22.0=h1bed415_0
+  - tk=8.6.7=hc745277_3
+  - tornado=4.5.3=py36_0
+  - wheel=0.30.0=py36hfd4bba0_1
+  - xz=5.2.3=h55aa19d_2
+  - zlib=1.2.11=ha838bed_2
+  - pip:
+    - "git+https://github.com/Neuroinflab/kCSD-python.git@master"
+

README.rst

@@ -0,0 +1,2 @@
+#!/bin/bash
+jupyter nbextension enable --py widgetsnbextension --sys-prefix