Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -21,14 +21,12 @@
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]]**
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.|
	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.|
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		-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.|
	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.|
32	32
33	33	=== Data analysis ===
34	34
...	...	@@ -44,11 +44,7 @@
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		-|**[[Brain-cockpit>>url:https://alexisthual.github.io/brain-cockpit/]]**
48		-Web-based application to explore large fMRI datasets and inter-subject alignments.|**[[Cobrawap>>url:https://cobrawap.readthedocs.io/]]**
49		-Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity.
50	50
51		-
52	52	=== Simulation ===
53	53
54	54	|[[**Arbor**>>url:https://docs.arbor-sim.org]]
...	...	@@ -77,14 +77,12 @@
77	77	"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.|
78	78
79	79	|**[[The Virtual Brain Web-App>>url:http://docs.thevirtualbrain.org/]]**
80		-The Virtual Brain Web App at HBP.|**[[NeuroR>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
81		-NeuroR is a collection of tools to repair morphologies.|**[[Local Field Potentials in Python>>url:https://lfpy.readthedocs.io/]]**
82		-LFPy is a Python module for the calculation of extracellular potentials and magnetic signals from activity in multicompartment neuron and network models.|
	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.|
83	83
84		-|**[[Snudda>>url:https://github.com/Hjorthmedh/Snudda/wiki]]**
85		-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]]**
86		-BlueNaaS-Subcellular is designed as a web based environment for the creation and simulation of reaction-diffusion models.
	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.
87	87
	78	+
	79	+
88	88	=== Neurorobotics ===
89	89
90	90	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**
...	...	@@ -93,21 +93,12 @@
93	93	=== Medical data analytics ===
94	94
95	95	|**[[Bids Manager & Pipeline>>url:https://github.com/Dynamap/BIDS_Manager]]**
96		-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]]**
97		-Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings:
98		-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]]**
99		-3D visualization software for intracranial EEG.|
	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.|
100	100
101		-|**[[ImaGIN>>url:https://wiki.ebrains.eu/bin/view/Collabs/quicknii-and-visualign]]**
102		-SPM-based Matlab toolbox for processing intracranial EEG recordings (SEEG and ECOG).|**[[IntranAt Electrodes>>url:https://intranat.readthedocs.io/]]**
103		-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]]**
104		-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.|
	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.
105	105
106		-|**[[Human Intracerebral EEG Platform (HIP)>>url:https://hip-infrastructure.github.io/build/html/index.html]]**
107		-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.
108	108
109		-
110		-
111	111	=== Neuromorphic computing ===
112	112
113	113	|**[[BrainScaleS>>url:https://wiki.ebrains.eu/bin/view/Collabs/neuromorphic/BrainScaleS/]]**
...	...	@@ -129,6 +129,7 @@
129	129	A plugin for SLURM used for the co-allocation of compute and data resources.|**[[Unicore>>url:https://www.unicore.eu/documentation/]]**
130	130	A set of software components for federated access to high-performance compute and data resources.|
131	131
	115	+
132	132	=== Support ===
133	133
134	134	Contact the [[EBRAINS High Level Support Team (HLST)>>https://ebrains.eu/support/]] if you have questions about our tools, services and workflows.