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21	21
22	22	=== Brain atlases ===
23	23
24		-|**[[PyJuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**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]]**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]]**
25		-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.|
	24	+|**[[PyJuGEx>>url:https://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/JuGex/JuGex_node.html]]**
	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]]**
	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.|
26	26	|**[[siibra-explorer>>url:https://siibra-explorer.readthedocs.io/en/latest/]]**
27	27	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/]]**
28		-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.
29		-|**[[VoluBA>>url:https://voluba-user-doc.apps-dev.hbp.eu/]]**VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
	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	+VoluBA (Volumetric Brain Anchoring) is an online service for anchoring of high-resolution volumes of interest from imaging experiments to very large reference volumes.|
30	30
31	31	=== Data analysis ===
32	32
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71	71	"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.|
72	72
73	73	|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
74		-The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://elephant.readthedocs.io/en/latest/index.html]]**NeuroR is a collection of tools to repair morphologies.|**[[Local Field Potentials in Python>>url:https://lfpy.readthedocs.io/]]**LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
	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/]]**
	78	+LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
75	75
76		-|**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**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.
	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.
77	77
78		-
79		-
80	80	=== Neurorobotics ===
81	81
82	82	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
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85	85	=== Medical data analytics ===
86	86
87	87	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
88		-Bids Manager is a tool that allows various users to easily import and explore databases in BIDS format. Bids Pipeline, an extension of Bids Manager, allows to launch process on BIDS database.|**[[Brainstorm>>url:https://neuroimage.usc.edu/brainstorm/Introduction]]**Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
89		-MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.|**[[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]**3D visualization software for intracranial EEG.|
	91	+Bids Manager is a tool that allows various users to easily import and explore databases in BIDS format. Bids Pipeline, an extension of Bids Manager, allows to launch process on BIDS database.|**[[Brainstorm>>url:https://neuroimage.usc.edu/brainstorm/Introduction]]**
	92	+Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
	93	+MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.|**[[HiBoP>>url:https://collab.humanbrainproject.eu/#/collab/78584/nav/531987?state=uuid%3Df72e40d9-a0bf-4ab7-8a27-462911107c5f]]**
	94	+3D visualization software for intracranial EEG.|
90	90
91		-|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**A software to visualize electrodes implantation on image data and prepare database for group studies.
	96	+|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
	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/]]**Web-based application to explore large fMRI datasets and inter-subject alignments.
92	92
93		-
94	94	=== Neuromorphic computing ===
95	95
96	96	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
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112	112	A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
113	113	A set of software components for federated access to high-performance compute and data resources.|
114	114
115		-
116	116	=== Support ===
117	117
118	118	Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.