Tools for Neuroscience & Immunology
For those who share our passion for neuroimmunology, here's a curated list of free online tools that we actively use in the lab
Atlases
EBRAINS - Explore detailed brain atlases for humans, monkeys, rats, and mice. These comprehensive maps help researchers understand brain structure, function, and connectivity, crucial for studying both healthy brains and neurological disorders.
Allen Brain Atlas - Atlases for the adult and developing mouse and human brains, as well as the mouse spinal cord.
Gene expression Atlas - Gene expression database that allows users to search across different species and biological conditions. It contains data from a variety of sources, including RNA-seq and microarray experiments.
Cell Type Taxonomies - This interactive explorer presents a multimodal cell census and atlas of primary motor cortex across human, marmoset and mouse species based on single-cell transcriptomic and epigenomic profiling.
Spectral Viewers
FluoroFinder - an interactive platform that helps design fluorescence experiments. It allows users to compare the spectral properties of different dyes and view instrument-specific laser and filter configurations.
Thermo Fisher Scientific's Fluorescence SpectraViewer - provides technical support and resources for the product, as well as information about the company.
BD Spectrum Viewer - a tool designed to aid flow cytometry panel design. It allows users to compare spectra of dyes and probes, choose filters, and assess potential issues with color overlap. It also offers pre-loaded cytometer configurations and the ability to save and share work.
Learning platforms
StereoInvestigator and Neurolucida - introduction to stereology and how Stereo Investigator can be used to perform stereological analysis to quantify the number, size, and shape of objects in tissue specimens.
Flow cytometry - introductory video to fluorescence-activated cell sorting (FACS)
Single-cell RNA sequencing - introductory video to 10x Chromium Single Cell Gene Expression Solution
ABBA - This video describes how to use ABBA to align serial brain sections to a 3D atlas (Allen Brain Atlas). Further detailed documentation can be found here.
Images obtained with Servier Medical Art licensed under CC BY 4.0