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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.|||
	36	+
33	33	=== Data analysis ===
34	34
35	35	|**[[Elephant>>url:https://elephant.readthedocs.io/en/latest/index.html]]**
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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
	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	+
55	55	=== Simulation ===
56	56
57	57	|[[**Arbor**>>url:https://docs.arbor-sim.org]]