Development of mGRASP for mapping mammalian synaptic connectivity

Knowledge of synaptic connectivity in complex neuronal circuits is crucial for understanding brain functions. Mammalian GFP reconstitution across synaptic partners (mGRASP) is a genetically-controlled, molecular engineering method to detect mammalian synapses using LM (Kim et al., 2012; Feng et al., 2012; 2014; Druckmann et al., 2014). It is based on two complementary split-GFP fragments (called spGFP1-10 and spGFP11), separately non-fluorescent, each tethered to synaptic membranes in each of two neuronal populations. When two neurons, each expressing one of the fragments, are closely opposed across a synaptic cleft, the split fragments unite and fluorescent GFP is reconstituted in that location. This molecular engineering approach allows the resolution, at nanometer-scale, of synapses viewable by LM.

eLemur: A cellular-resolution 3D atlas of the mouse lemur brain

Over the past decade, the vast majority of resources in basic and translational neuroscience has been directed to rodent model systems, following the assumption that universal principles apply across species. However, realistically, it is clear that many brain areas have species-specific structural and functional organizations, and further, that understanding complex human neurological disorders will require comparative approaches across model systems. The mouse lemur (Microcebus murinus), the world’s smallest primate, can contribute substantially to this comparison because of its evolutionary and genetic similarity to humans and rodents, its small brain size, and its rapid reproductive cycle. Here, to extend the utility of the mouse lemur as a model organism, we provide an advanced web-based brain atlas featuring both basic and detailed anatomical characteristics. Our work extends the coarse anatomical information available in existing stereotaxic, Nissl stain and MRI brain atlas of the mouse lemur by including many new details about cell types, laminar structures, and more.

Subthalamic input integration and deep brain stimulation

The subthalamic nuclues is known as an integrative information hubs within the basal ganglia, receiving extensive inputs from cortical and subcortical areas. Based on this characteristics, the subthalamic nucleus is the primary target for deep brain stimulation (DBS) which implement high frequency stimulation directly on the subthalamic nuclues. However, despite of decades long implication, circuit level mechanism underlying STN-DBS remains unknown, and even fundamental characteristics such as functional anatomy, molecular profiling and synaptic profiles of the STN circuitry are uncler due to the lack of systemic approaches. We thus provide detailed connectome description of excitatory and inhibitory inputs into the STN, using fluorescent protein-expressing viral tracers and mammlian GFP reconstitution across synaptic partner (mGRASP) for mapping connectivity of the STN at meso- and micro-scale, and commonly available Allen Connectivity Atals data set. We identified complex projection patterns in the STN from cortical regions and external globus pallidus.


Accurate morphological reconstruction of the sample neurons is necessary for turning our data into faithful biological knowledge. We have developed a reconstruction algorithm that is especially powerful for 3D fluorescence microscope data, as proven in the DIADEM challenge ( To get the morphology of neurite, which is also called tracing, there should be a start point or seed first. Then a cylinder is placed on the seed and its orientation and shape are adjusted automatically to maximize the correlation between the cylinder and the local intensity distribution.

neuTube is open source software for reconstructing neurons from fluorescence microscope images. The main function of neuTube is to generate a neuron structure from a 3D image with user interaction, which mainly consists of mouse clicks. It can also load SWC files from any other source for visualization or further editing.

How to cite:

Feng L, Zhao T*, and Kim J*, neuTube 1.0: A New Design for Efficient Neuron Reconstruction Software Based on The SWC Format, eNeuro, DOI: 10.1523/ENEURO.0049-14.2014.


mGRASP Puncta Detection Package

A Matlab package for detecting mGRASP puncta from microscope images.

How to cite:

Feng L, Kwon O., Lee B, Oh W., and Kim J* (2014). Using mammalian GFP reconstitution across synaptic partners (mGRASP) to map synaptic connectivity in the mouse brain. Nature Protocols 9, 2425-2437

Feng L, Zhao T*, and Kim J* (2012). Improved synapse detection for mGRASP-assistant connectivity mapping. Bioinformatics 28(12):25-31



mGRASP puncta detection package version 1.03

- Fix auto threshold search range

mGRASP puncta detection package version 1.02

- Add branch level mapping

- Fix threshold error

- Add scale_swc, save_swc, and save_puncta_as_apo functions

mGRASP puncta detection package version 1.01

- Fixed error when no soma is detected