Intro

The VCell (https://vcell.org/) application can export spatial simulation results into multiple formats, with .N5 (https://imagej.net/libs/n5) being one of them. N5 exports are stored remotely on VCell servers, allowing applications such as ImageJ to directly access the results of these simulations and perform analyses.

VCell Spatial Simulation

Simulation solvers generating 2- or 3-dimensional spatial domains can be visualized in ImageJ using this plugin. Spatial dimensions and time directly correspond to fields within an ImageJ image. The image's channels depict different variables within a simulation.

N5 and Datasets

Each N5 store is a direct mapping to a VCell simulation, and contains one or more datasets. Each dataset holds numerical data and metadata corresponding to an Image in ImageJ. Each N5 store is fully identified through its N5 URL which can be shared and opened by other applications which support the N5 format.

Accessing Simulation Results

For VCell exports generated from your local VCell installation:

From N5 URL (VCell Install Not Required):