Who We Are
Project Pipeline Support (PPS) works with Janelia Project Teams and labs to support large-scale project operation and the effective application of project workflows to lab investigations. PPS is currently made up of FlyLight Extension (FLE) and Connectomics Annotation (C&A).
FlyLight Extension continues the delivery of FlyLight pipeline output (labeled brains and light microscopy images) on demand to Janelia labs as the FlyLight Project Team ramps down.
Connectomics Annotation carries on from the Connectome Annotation Team (CAT) and Annotation & Analytics (A&A). We support the FlyEM Project Team and their collaboration with the Wellcome Trust, along with providing annotation services to Janelia labs. We generally operate at the synapse and whole neuron level. By contrast, the CellMap Project Team focuses more on a broad range of intracellular structures in cells and tissues.
PPS works closely with Project Technical Resources (PTR), sharing resources and coordinating support efforts as needed as they shrink and grow. PPS is geared to assist projects that are high-throughput and/or use established methods, and typically require a scheduling lead time of about 2 months. By contrast, PTR focuses on smaller projects that may be more developmental in nature, and strives to accommodate these on a more flexible time scale. PPS and PTR work closely together to find the best support solution for each project.
What We Do
C&A continues our ongoing efforts in the Drosophila electron microscopy (EM) datasets towards connectomes, potentially expanding to additional data types acquired using light microscopy (LM), video, audio and other modalities.
We perform annotation using software tools and applications developed in-house, or available commercially or as open source. We have expertise in CATMAID for tracing neurons and marking synapses (FlyTEM project), NeuTu, Neu3, and Neuroglancer for annotating neuron morphologies and connectomes (FlyEM project), and with this we advise Janelia lab heads on annotation strategies to meet specific project goals.
We continue to develop our capabilities in new technologies as they are developed or as driven by biology. Using data science, visualization and other analysis approaches, we aim to assist Janelia scientists in converting data to specific knowledge.
FlyLight developed standard pipelines for visualizing genetic driver lines using GAL4, LexA, split-GAL4, and split-LexA. Visualizations included general neuron morphology, synaptic labeling to determine neuronal polarity, and single cell labeling (MCFO). Crosses are scheduled in bulk by pipeline with the Fly Facility, followed by CNS dissection, immunohistochemistry, mounting, and high-quality confocal imaging. We use Zeiss LSM 700, 710, and 880 microscopes. Images can be delivered directly (as LSMs) or processed through alignment pipelines and organized in Janelia Workstation.
FlyLight Extension continues to offer these services to Janelia labs at large or small scale. Our core work continues to be the high-throughput screening of Initial Split (IS) GAL4 combinations to label specific subsets of neurons. The Fly Facility then makes a stable stock with the same split halves, and we verify its expression pattern. The Stable Split (SS) stock can then be further analyzed in our Polarity or MCFO pipelines. SS lines are a lasting resource for other purposes such as EASI-FISH (via PTR), single-cell sequencing, or electrophysiology.
We encourage collaborations on a wider range of projects, such as dissecting other species, using alternate labeling methods, etc.