Detailed summary of representative papers and important illustration candidates (Japanese)
[!NOTE] For the latest implementation status, please refer to Functional Implementation Status (Remaining Functionality).
Below are short summaries of representative papers and results that have had a large impact on connectome research, as well as potential illustrations and practical comments that may be worth excerpting from the published papers. If necessary, add DOI/links for each paper and Japanese translations of figure captions.
1) White et al., 1986 — The structure of the nervous system of Caenorhabditis elegans - Abstract: Systematically described the complete neuron/synapse connection diagram (so-called complete connectome) of C. elegans using an electron microscope. A classic result that provides the basis for studying the relationship between circuits and behavior at the individual level. - Candidate illustrations: full connection diagram (wire diagram), electron microscope image of a typical circuit, neuron number correspondence table. - Practical comments: "Gold standard" for small model models. Used as a benchmark for structure → function comparison.
2) Bock et al., 2011 — Network anatomy and in vivo physiology of visual cortical neurons - Abstract: A pioneering example of correlating the functions of the same neuron group with synaptic connections by combining in vivo functional measurements (calcium imaging/physiology) and high-resolution structural reconstruction based on EM. - Candidate illustrations: Functional response map and corresponding connection diagram based on EM reconstruction, EM enlarged image of a representative synapse. - Practical comments: A template for experimental design that integrates structure and function.
3) Kasthuri et al., 2015 — Saturated reconstruction of a volume of neocortex - Abstract: Report of a large-scale dataset showing synapse density, vesicle distribution, and complex wiring patterns between protrusions through saturated EM reconstruction of a small neocortex volume. - Candidate illustrations: 3D renderings of reconstructed volumes, synaptic density maps, and illustrative tracings of local circuits. - Practical comments: Important reference showing the actual situation of data size and processing cost.
4) Januszewski et al., 2018 — Flood-Filling Networks (FFN) for automated reconstruction - Abstract: An algorithmic breakthrough that introduces Flood-Filling Networks to significantly improve the accuracy of automatic neuron reconstruction from EM volumes. Reduce human proofreading burden. - Candidate illustrations: Comparison of FFN segmentation results (manual vs automatic), visualization of error types, processing flow diagram. - Practical comments: Core technology for automated pipelines. It is important to check the details of implementation and parameter adjustment.
5) Ronneberger et al., 2015 — U-Net for biomedical image segmentation - Abstract: U-Net has become a standard architecture for medical image segmentation and is widely applied for initial preprocessing of connectomes (membrane/cell boundary detection). - Picture candidate: U-Net structure diagram, segmentation sample (original image → prediction mask → post processing). - Practical comments: Essential as a segmentation basis. Transfer learning and self-supervised expansion are effective in practice.
6) Wickersham et al., 2007 — Monosynaptic restriction of transsynaptic tracing - Abstract: We present a monosynaptic restriction tracing method using a modified Labis virus. Tools for tracking specific input-output relationships in vivo. - Candidate illustration: Timeline of tracing experiment, infection route, and confirmation image of monosynaptic restriction. - Practical comment: Extremely effective for functional identification of circuit origins, but be aware of tracer limitations (range, toxicity).
7) FlyWire / Dorkenwald et al., 2024–2025 — Adult Drosophila whole-brain wiring diagram - Abstract: Using AI automatic segmentation + large-scale proofreading, we created and published a whole brain connectivity diagram (large number of neurons and tens of millions of synapses) of an adult Drosophila melanogaster. Can be explored on Codex and FlyWire platforms. - Candidate illustrations: Overall diagram of whole brain reconstruction, representative circuit/cell type annotation, synapse attribute distribution (number, area, neurotransmitter estimation). - Practical comments: Latest examples of large-scale connectome operations. Foundation for experimental analysis using data usage and API (Codex).
8) Schlegel et al., 2024 — Hemibrain / whole-brain annotation and cell typing - Abstract: Large-scale annotation of the FlyEM system and creation of a cell type atlas. A series of results showing connection types, circuit repeatability, and connection fingerprints for each cell type. - Candidate illustrations: cell type treemaps, network diagrams of typical modules/patterns. - Practical Comment: Reference data for linking cell type annotations and functional predictions.
9) Tavakoli et al., 2025 — Light-microscopy-based connectomic reconstruction (LICONN) - Abstract: Presents a method that combines optical methods (extension and special embedding) and deep learning segmentation to realize connectivity estimation from optical images (implementation example of connectivity estimation in large areas). - Candidate illustration: Comparison before and after optical/extension processing, cross-validation diagram of predicted connectivity and EM benchmark. - Practical comments: A practical example of an approach that preserves molecular information while reducing EM costs.
10) Sanfilippo et al., 2024 — Mapping neurotransmitter receptors to the connectome (example) - Abstract: An example of research that clarified the molecular background of synaptic function by linking receptor subtypes and protein complexes with the connectome. - Candidate illustrations: Superimposition of receptor distribution maps and synaptic connections, and diagrams of circuit differences by molecular profile. - Practical comment: Adding functional and molecular resolution improves the ability to interpret the connectome.
■ How to use and next output idea - Candidates for illustrations can be excerpts of high-resolution figures from papers with Japanese translation captions (be careful of citation rules and permissions). - Next task candidate (selectable): - a) Create a detailed list for each paper with DOI and paper link (and Japanese translation of citation captions for key figures) - b) Create a comparison table by comprehensively arranging papers on a specific theme (e.g. EM automatic segmentation) by year. - c) Select three of the above papers and create a Japanese translation slide plan for presentation slides based on the illustrations.
File creation date: 2026-03-18