Our recent paper “RapID Cell Counter: Semi-automated and mid-throughput estimation of cell density within diverse cortical layers” was published in eNeuro co-led by IGG grad students Aarthi Sekar and Thiago Sanches and in collaboration with the amazing Simó lab at UC Davis. After struggling to manually count neurons from images of in utero electroporation of mouse neocortex, we decided to make an easy-to-use automated tool that can quantify fluorescently-labeled cells across defined layers. The method is called RapID and is available here.

Some highlights of our study:

RapID runs as an easy-to-use GUI, with step-by-step instructions on how to install and run as supplementary materials and on the Github. Our hope is that the tool will be useful to the community with install and implementation representing only a small hurdle. Please reach out to us if you encounter difficulties!
Users define parameters for images based on expected cell size, density, and brightness. RapID subsequently will quantify labeled cells within a user-defined quadrangle (split by set number of layers). Parameters used for diverse cell types by our groups are included in the study as a starting point for users.
We successfully show that RapID results match manual “click” identification using Fiji’s Cell Counter and apply it to diverse cell images, including astrocytes and dopaminergic neurons.

As an added bonus: the beautiful images of dopaminergic neurons, made by the talented Keiko Hino and Sergi Simó, were selected as an official Zoom backdrop for the Society for Neuroscience available for download on their website!