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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/

    This is the classic MacOSX GUI for the CMTK registration tools (formerly called IGS suite). This is a frontend for software developed at https://www.nitrc.org/projects/cmtk. Please see http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui for instructions on how to carry out image registration.

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    ZENODO
    Software . 2011
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Nora Abi Akar; John Biddiscombe; Benjamin Cumming; Marko Kabic; +6 Authors

    Arbor Library Arbor library version 0.1, tagged as v0.1 Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models. An installation guide and library documentation are available online at Read the Docs. Submit a ticket if you have any questions or want help. Some key features include: * Optimized back ends for CUDA, KNL and AVX2 intrinsics. * Asynchronous spike exchange that overlaps compute and communication. * Efficient sampling of voltage and current on all back ends. * Efficient implementation of all features on GPU. * Reporting of memory and energy consumption (when available on platform). * An API for addition of new cell types, e.g. LIF and Poisson spike generators. * Validation tests against numeric/analytic models and NEURON. Contributors Nora Abi Akar John Biddiscombe Benjamin Cumming Marko Kabic Vasileios Karakasis Wouter Klijn Anne Küsters Ivan Martinez Alexander Peyser Stuart Yates

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    Software . 2018
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    Authors: Akar, Nora Abi; Biddiscombe, John; Cumming, Benjamin; Kabic, Marko; +19 Authors

    What's Changed Core API: Add S-Exp for CV Policies by @thorstenhater in #1511 Clean-up and extend mech cat iterator interface. by @thorstenhater in #1564 Mech ABI: The final step. by @thorstenhater in #1452 Add dim3 to gridDim constructor in generated mechanism code by @noraabiakar in #1630 Added an empty catalogue by @Helveg in #1677 Allow to limit Poisson schedule with a stop time (closes #1617) by @schmitts in #1684 Expose profiler to Python by @Helveg in #1688 Added a debug mode to build-catalogue by @Helveg in #1686 Write build-catalogue (c)make errors to stdout and stderr by @Helveg in #1679 Makejobs arg by @Helveg in #1673 Feature/python clean memory by @max9901 in #1670 Feature/label dict by @apeyser in #1711 Add locset expressions for proximal and distal translation of locations by @bcumming in #1671 Gap Junction mechanisms by @noraabiakar in #1682 Solve non-linear systems that are not kinetic schemes. by @noraabiakar in #1724 Add cos and sin SVE implementations by @noraabiakar in #1744 Deal with zero radius points in a morphology by @halfflat in #1719 Simplify default proc_allocation generation. by @halfflat in #1725 Find morphology location from a coordinate by @bcumming in #1751 resurrect lmorpho by @schmitts in #1746 Expose information about the CV discretization to the public inteface by @noraabiakar in #1758 Allow the use of string s-expression CV-policies in pyarb by @noraabiakar in #1799 Construct domain_decomposition given a list of group_descriptions. by @noraabiakar in #1788 Profile externally loaded mechanisms by @noraabiakar in #1691 Have option to set thread count to local maximum by @brenthuisman in #1716 CI/build/testing: Python unit test clean-up by @noraabiakar in #1595 Add CI for the in-repo Spack package by @schmitts in #1544 Ci/sanitize by @thorstenhater in #1521 Update spack package to include fmt for arbor@0.5.3: by @bcumming in #1609 Cache Spack for GHA by @schmitts in #1619 Run examples via scripts (closes #1566) by @schmitts in #1631 Build a catalogue in CI by @schmitts in #1632 Switch to PyPA's cibuildwheel action repo's. by @Helveg in #1703 Automatic test discovery sans boilerplate by @Helveg in #1693 build external mechanism catalogues in release mode by @noraabiakar in #1713 make VERBOSE=1 in verbose mode by @Helveg in #1715 Bump pybind to 2.8.1 by @brenthuisman in #1742 Better error reporting in python context interface by @bcumming in #1732 Better error diagnostic in python when invalid cell properties are provided. by @bcumming in #1743 Test separately built catalogues by @bcumming in #1748 Weekly cron job checking for submodule updates by @brenthuisman in #1741 Added local Python testsuite instructions by @Helveg in #1809 CMake CUDA clean-up. by @thorstenhater in #1804 Add dry run benchmark cell model for testing communication scaling by @bcumming in #1627 v0.6-rc by @brenthuisman in #1814 More robust build-catalogue by @thorstenhater in #1784 Documentation: arbor.mechanism_catalogue.extend() documentation added. by @brenthuisman in #1597 zenodo 0.5.2 entry by @brenthuisman in #1598 mpi.py updated for new synapse labelling by @brenthuisman in #1602 Tutorial structure: remove deduplication, includify by @brenthuisman in #1575 Docs mechabi by @brenthuisman in #1610 Improved documentation about weights by @brenthuisman in #1620 Adapt to changes in Pandas requiring unique indices by @brenthuisman in #1625 Add implies default license by @kanzl in #1635 Update Slack to Gitter by @brenthuisman in #1637 Better Python installation instructions by @brenthuisman in #1622 Add example based on LFPykit example Example_Arbor_swc.ipynb by @espenhgn in #1652 Name and describe arguments to constructors where ambiguous. by @brenthuisman in #1678 improved Github Issue templates by @brenthuisman in #1698 Add some comments about units to network ring examples by @schmitts in #1697 Fix link (closes #1664) by @schmitts in #1701 Fix class members in cable example by @schmitts in #1641 Correctify and seabornize dendrite tutorial by @brenthuisman in #1706 Polish GJ example readme by @thorstenhater in #1726 Completed the docs with more config() flags by @Helveg in #1708 Make connectivity example more complete by @brenthuisman in #1721 Add description of arbor and NEURON's nernst application rules to the docs. by @noraabiakar in #1638 Show docs version info more prominently on RTD by @brenthuisman in #1737 Update/fix tinyopt README.md by @halfflat in #1747 Add python gap junction example by @kanzl in #1750 Documentation: add expected nmodl units by @noraabiakar in #1756 Fixed broken link from get_probes to probes by @Helveg in #1763 Removed double preposition by @Helveg in #1762 Fixed MD to RST typo by @Helveg in #1760 Fix broken links in probe_sample.rst by @Helveg in #1761 Docs/contrib updates by @brenthuisman in #1736 Add Release procedure to docs by @brenthuisman in #1738 Example and tutorial for two cells connected via a gap junction by @schmitts in #1771 Have single source for citation info, compatible with Github citation UI by @brenthuisman in #1791 Advertise GH Discussions for modelling by @brenthuisman in #1793 Add release cycle info to docs by @brenthuisman in #1798 Added a warning when users are reading latest docs. by @Helveg in #1800 Fixes/optimization: Fix GPU compile. by @thorstenhater in #1601 Compile all arbor source files with -fvisibility=hidden by @noraabiakar in #1599 Bug/assorted static analysis by @thorstenhater in #1615 Fix ambiguous Region/Locset expressions by @thorstenhater in #1629 Clean-up AVX routine and global def [EOM] by @thorstenhater in #1618 Categorise ASSIGNED RANGE variables as STATE-ish. by @thorstenhater in #1624 Check that mechanisms have the right kind by @noraabiakar in #1633 Resolve uninitialised values. by @thorstenhater in #1616 Correctly parse diameter in ASCII files by @bcumming in #1640 Attempt fixing a64fx build by @bcumming in #1636 Fix simulation::add_sampler cell_group dispatch by @noraabiakar in #1654 Fix on-components on empty cable bug by @halfflat in #1658 Fix cv_policy parse and write in ACC by @noraabiakar in #1665 Fixed MRO and code duplication in setup.py by @Helveg in #1672 Rephrase exception message in case of missing segment by @schmitts in #1659 Fix modcc simd generation by @noraabiakar in #1681 Segfault on instantiating mechanisms on empty regions by @thorstenhater in #1657 Add missing closing bracket to mechanism repr (closes #1667) by @schmitts in #1699 Better handling of errors during dynamic catalogue loading by @thorstenhater in #1702 Swap && and || operator precedence in modcc by @noraabiakar in #1710 Remove use of removed INSTRUMENT_MALLOC symbols from Glibc 2.34 by @brenthuisman in #1730 Generate correct simd code for reading peer_index and v_peer by @noraabiakar in #1735 fixes for non-standard code by @boeschf in #1769 Modcc: Forward declare procedure kernels in generated GPU code by @noraabiakar in #1787 modcc: exit solvers early if errors encountered. by @noraabiakar in #1755 Fix cmake configuration of out-of-core fmt library by @bcumming in #1796 Bug fix: properly partition networks containing one-sided gap-junction connections by @noraabiakar

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    Software . 2021
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    Software . 2023
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    Software . 2022
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      Software . 2023
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      Software . 2022
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    Authors: Muhammad Fahad; Kim Sontheimer; Rolando Ingles; Wouter Klijn; +4 Authors

    The v2.0 official release of the Modular Science Framework for multi-scale Co-simulations. The main focus of this release is to improve the framework's usability and broaden its functionality, with a focus on integrating additional neuroscience use-cases. These include: Real-time calculation of Local Field Potentials (LFPs) based on spike events streamed from the NEST simulation. Integration of NEST Desktop, Insite pipeline, and Modular Science - Multiscale Co-simulation. Significant modifications have been implemented in the core modules, particularly RichEndpoint and Interscale Hub, with the aim of enhancing their efficiency, extensibility, and modularity to seamlessly accommodate forthcoming use-cases. The release notes for this release are available at Modular Science Framework v2.0.

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    Software . 2023
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    Software . 2023
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    Software . 2023
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    Authors: Huifang E WANG; Paul Triebkorn; Jean-Didier Lemaréchal; Jayant Jha; +6 Authors

    Codes: Delineating epileptogenic networks using brain imaging data and personalized modelling in drug-resistant epilepsy Precise estimates of the epileptogenic zone networks (EZN) are crucial for planning intervention strategies to treat drug resistant focal epilepsy. Here, we present the Virtual Epileptic Patient (VEP), a workflow that uses personalized brain models and machine learning methods to estimate the EZN and to aid the surgical strategy. The structural scaffold of the patient-specific whole brain network model is constructed from anatomical T1 and diffusion weighted MRI. Each network node is equipped with a mathematical dynamical model to simulate seizure activity. Bayesian inference methods sample and optimize key parameters of the personalized model using functional stereo-EEG recordings of patients’ seizures. These key parameters together with their personalized model determine a given patient’s EZN. The personalized model can further be used to predict the outcome of surgical intervention using virtual surgeries. The VEP workflow was evaluated retrospectively using 53 patients with drug resistant focal epilepsy. VEP reproduced the clinical definition with precision of 0.6, where the physical distance between epileptogenic regions identified by VEP and the clinically defined EZN was small. Compared with the resected brain regions of 25 patients who underwent surgery, VEP showed lower false discovery rates in seizure-free patients (mean: 0.028) than in not seizure-free patients (mean: 0.407). VEP is now being evaluated in an ongoing clinical trial (EPINOV) with expected 356 prospective epilepsy patients. {"references": ["Wang, H. E., Woodman, M., Triebkorn, P., Lemarechal, J.-D., Jha, J., Dollomaja, B., Vattikonda, A. N., Sip, V., Medina Villalon, S., Hashemi, M., Guye, M., Makhalova, J., Bartolomei, F., & Jirsa, V. (2023). Delineating epileptogenic networks using brain imaging data and personalized modeling in drug-resistant epilepsy. Science Translational Medicine, 15(680). https://doi.org/10.1126/scitranslmed.abp8982"]}

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    Authors: Deslauriers-Gauthier, Samuel; Frigo, Matteo; Zucchelli, Mauro; Deriche, Rachid;

    Python package that implements Tractograms As Linear Operators in Neuroimaging (TALON).

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    Authors: Pfeiffer, Paul; Tom��s, Federico Jos�� Barreda; Wu, Jiameng; Schleimer, Jan-Hendrik; +2 Authors

    Here, we demonstrate the capacitance clamp, a variant of the dynamic clamp technique to virtually modify capacitance in real excitable cells as described in "A dynamic clamp protocol to artificially modify cell capacitance". The repository contains instructions to establish the capacitance clamp in an electrophysiology setup, to run experiments with clamped cells, to analyse these experiments and finally to test and analyse the capacitance clamp in simulations.

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    Authors: Telenczuk; Rebollo; Navarro-Guzman; Sanchez-Vives; +1 Authors

    This python code simulates a mean-field model of two cortical columns, each described by a mean-field model comprising excitatory and inhibitory populations. The two columns are connected by electric-field interactions via current dipoles. See the details in the paper: Rebollo, B., Telenczuk, B., Navarro-Guzman, A., Destexhe, A. and Sanchez-Vives, M.V. Modulation of intercolumnar synchronization by endogeneous electric fields in cerebral cortex. Science Advances, 2021.

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    Authors: Alain Destexhe;

    Demo code for the kernel method to calculate LFPs from the spikes of a network of point neurons This demo shows the code to calculate the local field potential (LFP) generated by a network of point neurons. The kernel method calculates the LFP solely from the spikes of the neurons, and the knowledge of their position in space. This kernel method is explained in detail in the publication: Telenczuk, B., Telenczuk, M. and Destexhe, A. A kernel-based method to calculate local field potentials from networks of spiking neurons. bioRxiv preprint: https/www.biorxiv.org/content/10.1101/2020.03.29.014654v1 The program reads the raster of spike times, plots it, and then calculates the LFP, and plots it. The example provided is Brunel's model of gamma oscillations (the code reproduces Fig. 6 of the paper). Two versions are available: 1) A version in the hoc language used by the NEURON simulation environment. This version was written by Alain Destexhe. 2) A version in python 3 language, which does the same as the hoc version. This version was written by Bartosz Telenczuk. This demo is open-access, but please cite the original work if you use it. {"references": ["Telenczuk, B., Telenczuk, M. and Destexhe, A. A kernel-based method to calculate local field potentials from networks of spiking neurons. (under review in J Neurosci Methods) bioRxiv preprint: https/www.biorxiv.org/content/10.1101/2020.03.29.014654v1"]}

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    Authors: Bron, Esther E.;

    This project publishes the code used in the following publication: Bron et al., Cross-Cohort Generalizability of Deep and Conventional Machine Learning for MRI-based diagnosis and prediction of Alzheimer’s disease, NeuroImage: Clinical, 2021 Link: https://doi.org/10.1016/j.nicl.2021.102712, arxiv.org/2012.08769 Starting point: Overview.ipynb {"references": ["Bron et al., Cross-Cohort Generalizability of Deep and Conventional Machine Learning for MRI-based diagnosis and prediction of Alzheimer's disease, NeuroImage: Clinical, 2021"]} https://gitlab.com/radiology/neuro/bron-cross-cohort/-/tree/v1.0

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    This is the classic MacOSX GUI for the CMTK registration tools (formerly called IGS suite). This is a frontend for software developed at https://www.nitrc.org/projects/cmtk. Please see http://flybrain.mrc-lmb.cam.ac.uk/dokuwiki/doku.php?id=warping_manual:registration_gui for instructions on how to carry out image registration.

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    Authors: Nora Abi Akar; John Biddiscombe; Benjamin Cumming; Marko Kabic; +6 Authors

    Arbor Library Arbor library version 0.1, tagged as v0.1 Arbor is a library for implementing performance portable network simulations of multi-compartment neuron models. An installation guide and library documentation are available online at Read the Docs. Submit a ticket if you have any questions or want help. Some key features include: * Optimized back ends for CUDA, KNL and AVX2 intrinsics. * Asynchronous spike exchange that overlaps compute and communication. * Efficient sampling of voltage and current on all back ends. * Efficient implementation of all features on GPU. * Reporting of memory and energy consumption (when available on platform). * An API for addition of new cell types, e.g. LIF and Poisson spike generators. * Validation tests against numeric/analytic models and NEURON. Contributors Nora Abi Akar John Biddiscombe Benjamin Cumming Marko Kabic Vasileios Karakasis Wouter Klijn Anne Küsters Ivan Martinez Alexander Peyser Stuart Yates

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    Software . 2018
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    Authors: Akar, Nora Abi; Biddiscombe, John; Cumming, Benjamin; Kabic, Marko; +19 Authors

    What's Changed Core API: Add S-Exp for CV Policies by @thorstenhater in #1511 Clean-up and extend mech cat iterator interface. by @thorstenhater in #1564 Mech ABI: The final step. by @thorstenhater in #1452 Add dim3 to gridDim constructor in generated mechanism code by @noraabiakar in #1630 Added an empty catalogue by @Helveg in #1677 Allow to limit Poisson schedule with a stop time (closes #1617) by @schmitts in #1684 Expose profiler to Python by @Helveg in #1688 Added a debug mode to build-catalogue by @Helveg in #1686 Write build-catalogue (c)make errors to stdout and stderr by @Helveg in #1679 Makejobs arg by @Helveg in #1673 Feature/python clean memory by @max9901 in #1670 Feature/label dict by @apeyser in #1711 Add locset expressions for proximal and distal translation of locations by @bcumming in #1671 Gap Junction mechanisms by @noraabiakar in #1682 Solve non-linear systems that are not kinetic schemes. by @noraabiakar in #1724 Add cos and sin SVE implementations by @noraabiakar in #1744 Deal with zero radius points in a morphology by @halfflat in #1719 Simplify default proc_allocation generation. by @halfflat in #1725 Find morphology location from a coordinate by @bcumming in #1751 resurrect lmorpho by @schmitts in #1746 Expose information about the CV discretization to the public inteface by @noraabiakar in #1758 Allow the use of string s-expression CV-policies in pyarb by @noraabiakar in #1799 Construct domain_decomposition given a list of group_descriptions. by @noraabiakar in #1788 Profile externally loaded mechanisms by @noraabiakar in #1691 Have option to set thread count to local maximum by @brenthuisman in #1716 CI/build/testing: Python unit test clean-up by @noraabiakar in #1595 Add CI for the in-repo Spack package by @schmitts in #1544 Ci/sanitize by @thorstenhater in #1521 Update spack package to include fmt for arbor@0.5.3: by @bcumming in #1609 Cache Spack for GHA by @schmitts in #1619 Run examples via scripts (closes #1566) by @schmitts in #1631 Build a catalogue in CI by @schmitts in #1632 Switch to PyPA's cibuildwheel action repo's. by @Helveg in #1703 Automatic test discovery sans boilerplate by @Helveg in #1693 build external mechanism catalogues in release mode by @noraabiakar in #1713 make VERBOSE=1 in verbose mode by @Helveg in #1715 Bump pybind to 2.8.1 by @brenthuisman in #1742 Better error reporting in python context interface by @bcumming in #1732 Better error diagnostic in python when invalid cell properties are provided. by @bcumming in #1743 Test separately built catalogues by @bcumming in #1748 Weekly cron job checking for submodule updates by @brenthuisman in #1741 Added local Python testsuite instructions by @Helveg in #1809 CMake CUDA clean-up. by @thorstenhater in #1804 Add dry run benchmark cell model for testing communication scaling by @bcumming in #1627 v0.6-rc by @brenthuisman in #1814 More robust build-catalogue by @thorstenhater in #1784 Documentation: arbor.mechanism_catalogue.extend() documentation added. by @brenthuisman in #1597 zenodo 0.5.2 entry by @brenthuisman in #1598 mpi.py updated for new synapse labelling by @brenthuisman in #1602 Tutorial structure: remove deduplication, includify by @brenthuisman in #1575 Docs mechabi by @brenthuisman in #1610 Improved documentation about weights by @brenthuisman in #1620 Adapt to changes in Pandas requiring unique indices by @brenthuisman in #1625 Add implies default license by @kanzl in #1635 Update Slack to Gitter by @brenthuisman in #1637 Better Python installation instructions by @brenthuisman in #1622 Add example based on LFPykit example Example_Arbor_swc.ipynb by @espenhgn in #1652 Name and describe arguments to constructors where ambiguous. by @brenthuisman in #1678 improved Github Issue templates by @brenthuisman in #1698 Add some comments about units to network ring examples by @schmitts in #1697 Fix link (closes #1664) by @schmitts in #1701 Fix class members in cable example by @schmitts in #1641 Correctify and seabornize dendrite tutorial by @brenthuisman in #1706 Polish GJ example readme by @thorstenhater in #1726 Completed the docs with more config() flags by @Helveg in #1708 Make connectivity example more complete by @brenthuisman in #1721 Add description of arbor and NEURON's nernst application rules to the docs. by @noraabiakar in #1638 Show docs version info more prominently on RTD by @brenthuisman in #1737 Update/fix tinyopt README.md by @halfflat in #1747 Add python gap junction example by @kanzl in #1750 Documentation: add expected nmodl units by @noraabiakar in #1756 Fixed broken link from get_probes to probes by @Helveg in #1763 Removed double preposition by @Helveg in #1762 Fixed MD to RST typo by @Helveg in #1760 Fix broken links in probe_sample.rst by @Helveg in #1761 Docs/contrib updates by @brenthuisman in #1736 Add Release procedure to docs by @brenthuisman in #1738 Example and tutorial for two cells connected via a gap junction by @schmitts in #1771 Have single source for citation info, compatible with Github citation UI by @brenthuisman in #1791 Advertise GH Discussions for modelling by @brenthuisman in #1793 Add release cycle info to docs by @brenthuisman in #1798 Added a warning when users are reading latest docs. by @Helveg in #1800 Fixes/optimization: Fix GPU compile. by @thorstenhater in #1601 Compile all arbor source files with -fvisibility=hidden by @noraabiakar in #1599 Bug/assorted static analysis by @thorstenhater in #1615 Fix ambiguous Region/Locset expressions by @thorstenhater in #1629 Clean-up AVX routine and global def [EOM] by @thorstenhater in #1618 Categorise ASSIGNED RANGE variables as STATE-ish. by @thorstenhater in #1624 Check that mechanisms have the right kind by @noraabiakar in #1633 Resolve uninitialised values. by @thorstenhater in #1616 Correctly parse diameter in ASCII files by @bcumming in #1640 Attempt fixing a64fx build by @bcumming in #1636 Fix simulation::add_sampler cell_group dispatch by @noraabiakar in #1654 Fix on-components on empty cable bug by @halfflat in #1658 Fix cv_policy parse and write in ACC by @noraabiakar in #1665 Fixed MRO and code duplication in setup.py by @Helveg in #1672 Rephrase exception message in case of missing segment by @schmitts in #1659 Fix modcc simd generation by @noraabiakar in #1681 Segfault on instantiating mechanisms on empty regions by @thorstenhater in #1657 Add missing closing bracket to mechanism repr (closes #1667) by @schmitts in #1699 Better handling of errors during dynamic catalogue loading by @thorstenhater in #1702 Swap && and || operator precedence in modcc by @noraabiakar in #1710 Remove use of removed INSTRUMENT_MALLOC symbols from Glibc 2.34 by @brenthuisman in #1730 Generate correct simd code for reading peer_index and v_peer by @noraabiakar in #1735 fixes for non-standard code by @boeschf in #1769 Modcc: Forward declare procedure kernels in generated GPU code by @noraabiakar in #1787 modcc: exit solvers early if errors encountered. by @noraabiakar in #1755 Fix cmake configuration of out-of-core fmt library by @bcumming in #1796 Bug fix: properly partition networks containing one-sided gap-junction connections by @noraabiakar

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