This code uses OpenFrameworks v0.9.8 to visualize hundreds of different RNA molecules in neurons from an intact mouse hippocampus.
The ExSeq pre-print, Alon et al 2020, is now available ! The ExSeqProcessing library, which is your first step in converting multi-round RNA imaging into 3D-localized RNA molecules, is available here.
To get running, you must download OpenFramworks v.0.9.8 and put the ExSeqViewer2 folder from this repository into the "apps" folder.
OpenFrameworks is a tremendously powerful tool written entirely by a collaborative, open source community. We, the authors of ExSeq, are grateful for this foundation and are happy to demonstrate its use in a scientific context. While it might be confusing at first to get started with OpenFrameworks, it comes packaged with an excellent set of examples that should run right out of the box. Playing with examples is how you learn to use OpenFrameworks!
While this is all the code we used, this code must be treated as "research-grade." Please do not hesitate to post comments or questions!