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24	24	|**[[PyJuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
25	25	Find a set of differentially expressed genes between two user defined volumes of interest based on JuBrain maps.|**[[Julich-Brain Gene Expression>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
26		-Decoding the chain from genes to cognition requires detailed insights how areas with specific gene activities and microanatomical architectures contribute to brain function and dysfunction.|**[[QuickNII>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
	26	+Decoding the chain from genes to cognition requires detailed insights how areas with specific gene activities and microanatomical architectures contribute to brain function and dysfunction.|**[[QuickNII>>url:https://quicknii.readthedocs.io]]**
27	27	QuickNII is a tool for user guided affine registration (anchoring) of 2D experimental image data, typically high resolution microscopic images, to 3D atlas reference space, facilitating data integration through standardized coordinate systems.|
	28	+
28	28	|**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
29	29	siibra-explorer is a browser-based viewer for the visual exploration of the EBRAINS atlases at microscopic detail, as well as the discovery of related multimodal data features. It is tightly integrated with the EBRAINS Knowledge Graph, allowing the seamless querying of semantically and spatially anchored datasets.|**[[siibra-python>>url:https://siibra-python.readthedocs.io/en/latest/]]**
30	30	siibra-python is a comprehensive Python client providing access to EBRAINS atlases and offering an easy and well-structured way to include maps, reference templates, region definitions and linked datasets in reproducible programmatic workflows.|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**
31	31	VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
32	32
	34	+|**[[VisuAlign>>url:https://visualign.readthedocs.io]]**
	35	+VisuAlign is a tool for applying user-guided nonlinear refinements (inplane) to an existing, affine 2D-to-3D registration, such as created using QuickNII.| | |
	36	+
33	33	=== Data analysis ===
34	34
35	35	|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
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36	36	Elephant is an open-source Python library for the analysis of neurophysiology data, using Neo data structures.|**[[HBP Validation Framework - Python Client>>url:http://hbp-validation-client.readthedocs.io/]]**
37	37	A Python package for working with the Human Brain Project Model Validation Framework.|**[[Neo>>url:https://neo.readthedocs.io/en/stable/]]**
38	38	an object model for handling electrophysiology data in multiple formats.|
	43	+
39	39	|**[[Neo Viewer>>url:https://neo-viewer.brainsimulation.eu/]]**
40	40	Django/Angular software for graphing neural activity data (analog signals, spike trains etc.) read from Neo files.|**[[NeuroScheme>>url:https://neuroscheme-documentation.readthedocs.io/en/latest/]]**
41	41	NeuroScheme is a tool for navigating, exploring, creating and interacting with NeuroScience data using abstract, schematic or expressive representations.|**[[NeuroTessMesh>>url:https://neurotessmesh-documentation.readthedocs.io/en/latest/]]**
42	42	A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
43		-|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
	48	+
	49	+|**[[Nutil>>url:https://nutil.readthedocs.io/en/latest/]]**
44	44	Nutil aims to both simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat.|**[[ViSimpl>>url:https://visimpl-documentation.readthedocs.io/en/latest/]]**
45	45	ViSimpl integrates a set of visualization and interaction tools that provide a multi-view visual analysis of brain simultation data.|**[[ilastik>>url:http://ilastik.org/documentation/index.html]]**
46	46	ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
47	47
	54	+|**[[Brain-cockpit>>url:https://alexisthual.github.io/brain-cockpit/]]**
	55	+Web-based application to explore large fMRI datasets and inter-subject alignments.|**[[Cobrawap>>url:https://cobrawap.readthedocs.io/]]**
	56	+Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity.|**[[Viziphant>>url:https://viziphant.readthedocs.io/en/latest/index.html]]**
	57	+Viziphant provides an easy way to generate plots and interactive visualizations of neuroscientific data and analysis results|
	58	+
	59	+|**[[MeshView>>url:https://meshview-for-brain-atlases.readthedocs.io]]**
	60	+MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain.|**[[LocaliZoom>>url:https://localizoom.readthedocs.io/en/latest/]]**
	61	+Web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases.| |
	62	+
48	48	=== Simulation ===
49	49
50	50	|[[**Arbor**>>url:https://docs.arbor-sim.org]]
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73	73	"The Virtual Brain" Project (TVB Project) has the purpose of offering modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains, brains modeled at the level of population of neurons.|
74	74
75	75	|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
76		-The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
77		-NeuroR is a collection of tools to repair morphologies.|**[[Local Field Potentials in Python>>url:https://lfpy.readthedocs.io/]]**
	91	+The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://neuror.readthedocs.io/]]**
	92	+NeuroR is a collection of tools to repair morphologies.|**[[LFPy>>url:https://lfpy.readthedocs.io/]]**
78	78	LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
79	79
80	80	|**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**
81		-Snudda is a tool that allows the user to place neurons within multiple volumes, then performs touch detection to infer where putative synapses are based on reconstructed neuron morphologies.
	96	+Snudda is a tool that allows the user to place neurons within multiple volumes, then performs touch detection to infer where putative synapses are based on reconstructed neuron morphologies.|**[[BlueNaaS-Subcellular>>url:https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html]]**
	97	+BlueNaaS-Subcellular is designed as a web based environment for the creation and simulation of reaction-diffusion models.|**[[libsonata>>url:https://libsonata.readthedocs.io/en/stable/]]**
	98	+A C++ / Python API for reading SONATA circuit files.|
82	82
83	83	=== Neurorobotics ===
84	84
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95	95
96	96	|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
97	97	SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**
98		-A software to visualize electrodes implantation on image data and prepare database for group studies.|**[[Brain-cockpit>>url:https://alexisthual.github.io/brain-cockpit/]]**
99		-Web-based application to explore large fMRI datasets and inter-subject alignments.
	115	+A software to visualize electrodes implantation on image data and prepare database for group studies.|**[[Medical Informatics Platform (MIP)>>url:https://github.com/HBPMedical/mip-docs]]**
	116	+The MIP is an open-source platform enabling federated data analysis in a secure environment for centers interested in initiating or joining disease-oriented federations with the aim of analyzing large-scale distributed clinical datasets.|
100	100
	118	+|**[[Human Intracerebral EEG Platform (HIP)>>url:https://hip-infrastructure.github.io/build/html/index.html]]**
	119	+The HIP is a state-of-the-art open-source platform, offering integrated tools and workflows for optimized collection, storage, sharing, processing and analysis of multiscale Human intracerebral EEG data.
	120	+
101	101	=== Neuromorphic computing ===
102	102
103	103	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**