Epic: N5 and VCell ImageJ plugin Minimal Viable Product

[jcschaff]

Minimal Viable Product for a ImageJ plugin for VCell which can extract data from VCell servers using S3 and N5.

Motivation

It would be powerful for many users to be able to compare spatial simulation data and microscopy data in a familiar shared environment. The ImageJ application provides a platform where images can be viewed, processed and compared. Making VCell spatial simulation data as images within ImageJ would be a convenient and familiar way to compare simulation results with spatial data.

Completion Criteria

• VCell Client users should be able to select simulation data to be made available to the VCell ImageJ Plugin as images for viewing and processing.
• The VCell ImageJ plugin should allow users to open these datasets within ImageJ without downloading the entire dataset.
• documentation should be provided.
• together, this capability should be a minimal viable product (MVP) for ImageJ/VCell integration mediated through the vcell servers.

Essential Stories/Tasks

• [x] https://github.com/virtualcell/vcell/issues/1071
• [x] #19
• [x] https://github.com/virtualcell/vcell/issues/1072
• [x] #13

Future

• 31

[jcschaff]

added @vcellmike's Update VCell help to delete ImageJ references#1056 to task list.

[AvocadoMoon]

Architecture of export is up in alpha, next steps.

• Make it easier to understand what you've exported and that this exists
• A loader that displays the time it takes to load an image, giving users feedback

[AvocadoMoon]

Direct line to most recent export can still have table, but the user who doesn't want to use it doesn't need to know about it.

[AvocadoMoon]

Was able to do a live demo at a conference with the tool. It works, but still isn't polished to the point of a finished product.