Research dissecting the functional organization of the brain is a rapidly growing area of study, buoyed by support from major federal initiatives. However, neuroscience software infrastructure has lagged behind; notably, the most powerful software often require computational expertise beyond the scope of most labs. Here, we introduce an easy-to-use yet powerful neuroscience software that overcomes these limitations by leveraging a modern software architecture. BioImage Suite Web (BISWeb; https://bioimagesuiteweb.github.io/webapp/) is a point-and-click app that runs in any modern web browser without any installation necessary, yet with performance rivaling that of a locally installed software. Due to the general nature of its architecture (C++, WebAssembly, JavaScript), BISWeb works on most modern web-browsers, major operating systems, and devices. Importantly, this architecture is flexible—algorithms can also be used through command line tools and toolkits for external environments (currently Python and Matlab). BISWeb currently supports a range of functionality in human and animal neuroscience, from defacing to connectome visualization. A feature is the use of a formal description (JSON) to define module inputs, outputs, and parameters. This information is used internally and can also be saved by the user, enabling a workflow in which a user can return to work later, share work with collaborators as “live figures”, validate analyses, and validate software across updates. A wealth of information is available for users at all skill levels, and all code will remain openly available. Overall, BISWeb highlights the advantages of a modern software architecture: accessibility, transparency, reproducibility.