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9	9	=== Find data ===
10	10
11	11	|**[[EBRAINS Knowledge Graph>>url:https://kg.ebrains.eu/]]**
12		-A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.|**[[KnowledgeSpace>>url:https://knowledge-space.org/documentation]]**
	12	+A user-driven, data-sharing and data-management infrastructure accelerating scientific progress by providing access to large collections of curated, heterogeneous neuroscience data.|**[[KnowledgeSpace>>https://knowledge-space.org/documentation/#what_is_ks]]**
13	13	Encyclopedia and open data access portal for neuroscience that serves as a framework where large-scale neuroscience projects can expose their data to the neuroscience community-at-large.|**[[fairgraph>>url:https://fairgraph.readthedocs.io/en/latest/]]**
14	14	Python API for the Human Brain Project Neural Activity Resource, capable of changing, and working with Metadata|
15	15
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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	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.|**[[WebAlign>>url:https://webalign.readthedocs.io]]**
	36	+WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.|**[[WebWarp>>url:https://webwarp.readthedocs.io/en/latest/index.html]]**
	37	+WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases.|
	38	+
33	33	=== Data analysis ===
34	34
35	35	|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
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42	42	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/]]**
43	43	A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement|
44	44
45		-|**[[Nutil>>url:https://wiki.ebrains.eu/bin/view/Collabs/quint]]**
	51	+|**[[Nutil>>url:https://nutil.readthedocs.io/en/latest/]]**
46	46	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/]]**
47	47	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]]**
48	48	ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis.|
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52	52	Cobrawap is a Python-based, adaptable, and reusable pipeline for analyzing cortical wave activity.|**[[Viziphant>>url:https://viziphant.readthedocs.io/en/latest/index.html]]**
53	53	Viziphant provides an easy way to generate plots and interactive visualizations of neuroscientific data and analysis results|
54	54
	61	+|**[[MeshView>>url:https://meshview-for-brain-atlases.readthedocs.io]]**
	62	+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/]]**
	63	+Web application for viewing of series of high-resolution 2D images that have been anchored to reference atlases.| |
	64	+
55	55	=== Simulation ===
56	56
57	57	|[[**Arbor**>>url:https://docs.arbor-sim.org]]
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89	89	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/]]**
90	90	A C++ / Python API for reading SONATA circuit files.|
91	91
	102	+|**[[Brain Scaffold Builder>>url:https://bsb.readthedocs.io/]]**
	103	+The BSB is a framework for reconstructing and simulating multi-paradigm neuronal network models. It removes much of the repetitive work associated with writing the required code and lets you focus on the parts that matter. It helps write organized, well-parametrized and explicit code understandable and reusable by your peers.|**[[InSite>>url:https://vrgrouprwth.github.io/insite/]]**
	104	+Insite provides a middleware that enables users to acquire data from NEST, Abror and TVB via the in-transit paradigm.|**[[IntraCellular Pathway Modeling>>url:https://github.com/icpm-kth]]**
	105	+Tools for data-driven building of subcellular biochemical signaling pathway models, including interoperable modules for model building, calibration, and model analysis.|
	106	+
	107	+
92	92	=== Neurorobotics ===
93	93
94	94	|**[[Neurorobotics Platform>>url:https://www.neurorobotics.net/Documentation/nrp/user_manual/index.html]]**