@article {68709, title = {BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature Methods}, volume = {20}, year = {2023}, month = {2023 Jun 01}, abstract = {

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

}, issn = {1548-7105}, doi = {10.1038/s41592-023-01848-5}, author = {Manubens-Gil, Linus and Zhou, Zhi and Chen, Hanbo and Ramanathan, Arvind and Liu, Xiaoxiao and Liu, Yufeng and Bria, Alessandro and Gillette, Todd and Ruan, Zongcai and Yang, Jian and Radojevi{\'c}, Miroslav and Zhao, Ting and Cheng, Li and Qu, Lei and Liu, Siqi and Bouchard, Kristofer E and Gu, Lin and Cai, Weidong and Ji, Shuiwang and Roysam, Badrinath and Wang, Ching-Wei and Yu, Hongchuan and Sironi, Amos and Iascone, Daniel Maxim and Zhou, Jie and Bas, Erhan and Conde-Sousa, Eduardo and Aguiar, Paulo and Li, Xiang and Li, Yujie and Nanda, Sumit and Wang, Yuan and Muresan, Leila and Fua, Pascal and Ye, Bing and He, Hai-Yan and Staiger, Jochen F and Peter, Manuel and Cox, Daniel N and Simonneau, Michel and Oberlaender, Marcel and Jefferis, Gregory and Ito, Kei and Gonzalez-Bellido, Paloma and Kim, Jinhyun and Rubel, Edwin and Cline, Hollis T and Zeng, Hongkui and Nern, Aljoscha and Chiang, Ann-Shyn and Yao, Jianhua and Roskams, Jane and Livesey, Rick and Stevens, Janine and Liu, Tianming and Dang, Chinh and Guo, Yike and Zhong, Ning and Tourassi, Georgia and Hill, Sean and Hawrylycz, Michael and Koch, Christof and Meijering, Erik and Ascoli, Giorgio A and Peng, Hanchuan} } @article {6828, title = {A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.}, journal = {Cell Reports}, volume = {3}, year = {2013}, month = {2013 May 30}, pages = {1739-53}, abstract = {

How the brain perceives sensory information and generates meaningful behavior depends critically on its underlying circuitry. The protocerebral bridge (PB) is a major part of the insect central complex (CX), a premotor center that may be analogous to the human basal ganglia. Here, by deconstructing hundreds of PB single neurons and reconstructing them into a common three-dimensional framework, we have constructed a comprehensive map of PB circuits with labeled polarity and predicted directions of information flow. Our analysis reveals a highly ordered information processing system that involves directed information flow among CX subunits through 194 distinct PB neuron types. Circuitry properties such as mirroring, convergence, divergence, tiling, reverberation, and parallel signal propagation were observed; their functional and evolutional significance is discussed. This layout of PB neuronal circuitry may provide guidelines for further investigations on transformation of sensory (e.g., visual) input into locomotor commands in fly brains.

}, keywords = {Animals, Biological, Brain, Drosophila, Models, Neurons}, issn = {2211-1247}, doi = {10.1016/j.celrep.2013.04.022}, author = {Lin, Chih-Yung and Chuang, Chao-Chun and Hua, Tzu-En and Chen, Chun-Chao and Dickson, Barry J and Greenspan, Ralph J and Chiang, Ann-Shyn} } @article {6827, title = {Parallel neural pathways mediate CO2 avoidance responses in Drosophila.}, journal = {Science}, volume = {340}, year = {2013}, month = {2013 Jun 14}, pages = {1338-41}, abstract = {

Different stimulus intensities elicit distinct perceptions, implying that input signals are either conveyed through an overlapping but distinct subpopulation of sensory neurons or channeled into divergent brain circuits according to intensity. In Drosophila, carbon dioxide (CO2) is detected by a single type of olfactory sensory neuron, but information is conveyed to higher brain centers through second-order projection neurons (PNs). Two distinct pathways, PN(v)-1 and PN(v)-2, are necessary and sufficient for avoidance responses to low and high CO2 concentrations, respectively. Whereas low concentrations activate PN(v)-1, high concentrations activate both PN(v)s and GABAergic PN(v)-3, which may inhibit PN(v)-1 pathway-mediated avoidance behavior. Channeling a sensory input into distinct neural pathways allows the perception of an odor to be further modulated by both stimulus intensity and context.

}, keywords = {Animals, Carbon Dioxide, Drosophila melanogaster, Escape Reaction, Olfactory Pathways, Olfactory Receptor Neurons}, issn = {1095-9203}, doi = {10.1126/science.1236693}, author = {Lin, Hui-Hao and Chu, Li-An and Fu, Tsai-Feng and Dickson, Barry J and Chiang, Ann-Shyn} } @article {47222, title = {Heterotypic gap junctions between two neurons in the drosophila brain are critical for memory.}, journal = {Current Biology : CB}, volume = {21}, year = {2011}, month = {2011 May 24}, pages = {848-54}, abstract = {

Gap junctions play an important role in the regulation of neuronal metabolism and homeostasis by serving as connections that enable small molecules to pass between cells and synchronize activity between cells. Although recent studies have linked gap junctions to memory formation, it remains unclear how they contribute to this process. Gap junctions are hexameric hemichannels formed from the connexin and pannexin gene families in chordates and the innexin (inx) gene family in invertebrates. Here we show that two modulatory neurons, the anterior paired lateral (APL) neuron and the dorsal paired medial (DPM) neuron, form heterotypic gap junctions within the mushroom body (MB), a learning and memory center in the Drosophila brain. Using RNA interference-mediated knockdowns of inx7 and inx6 in the APL and DPM neurons, respectively, we found that flies showed normal olfactory associative learning and intact anesthesia-resistant memory (ARM) but failed to form anesthesia-sensitive memory (ASM). Our results reveal that the heterotypic gap junctions between the APL and DPM neurons are an essential part of the MB circuitry for memory formation, potentially constituting a recurrent neural network to stabilize ASM.

}, keywords = {Anesthesia, Animals, Animals, Genetically Modified, Connexins, Drosophila, Drosophila Proteins, Gap Junctions, Memory, Mushroom Bodies, Neurons, RNA Interference, Smell}, issn = {1879-0445}, doi = {10.1016/j.cub.2011.02.041}, author = {Wu, Chia-Lin and Shih, Meng-Fu Maxwell and Lai, Jason Sih-Yu and Yang, Hsun-Ti and Turner, Glenn C and Chen, Linyi and Chiang, Ann-Shyn} } @article {4304, title = {Serotonin-mushroom body circuit modulating the formation of anesthesia-resistant memory in Drosophila.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, year = {2011}, month = {2011 Aug 16}, pages = {13794-9}, abstract = {

Pavlovian olfactory learning in Drosophila produces two genetically distinct forms of intermediate-term memories: anesthesia-sensitive memory, which requires the amnesiac gene, and anesthesia-resistant memory (ARM), which requires the radish gene. Here, we report that ARM is specifically enhanced or inhibited in flies with elevated or reduced serotonin (5HT) levels, respectively. The requirement for 5HT was additive with the memory defect of the amnesiac mutation but was occluded by the radish mutation. This result suggests that 5HT and Radish protein act on the same pathway for ARM formation. Three supporting lines of evidence indicate that ARM formation requires 5HT released from only two dorsal paired medial (DPM) neurons onto the mushroom bodies (MBs), the olfactory learning and memory center in Drosophila: (i) DPM neurons were 5HT-antibody immunopositive; (ii) temporal inhibition of 5HT synthesis or release from DPM neurons, but not from other serotonergic neurons, impaired ARM formation; (iii) knocking down the expression of d5HT1A serotonin receptors in α/β MB neurons, which are innervated by DPM neurons, inhibited ARM formation. Thus, in addition to the Amnesiac peptide required for anesthesia-sensitive memory formation, the two DPM neurons also release 5HT acting on MB neurons for ARM formation.

}, issn = {1091-6490}, doi = {10.1073/pnas.1019483108}, author = {Lee, Pei-Tseng and Lin, Hsuan-Wen and Chang, Yu-Hsuan and Fu, Tsai-Feng and Dubnau, Josh and Hirsh, Jay and Lee, Tzumin and Chiang, Ann-Shyn} } @article {792, title = {Gradients of the Drosophila Chinmo BTB-zinc finger protein govern neuronal temporal identity.}, journal = {Cell}, volume = {127}, year = {2006}, month = {2006 Oct 20}, pages = {409-22}, abstract = {

Many neural progenitors, including Drosophila mushroom body (MB) and projection neuron (PN) neuroblasts, sequentially give rise to different subtypes of neurons throughout development. We identified a novel BTB-zinc finger protein, named Chinmo (Chronologically inappropriate morphogenesis), that governs neuronal temporal identity during postembryonic development of the Drosophila brain. In both MB and PN lineages, loss of Chinmo autonomously causes early-born neurons to adopt the fates of late-born neurons from the same lineages. Interestingly, primarily due to a posttranscriptional control, MB neurons born at early developmental stages contain more abundant Chinmo than their later-born siblings. Further, the temporal identity of MB progeny can be transformed toward earlier or later fates by reducing or increasing Chinmo levels, respectively. Taken together, we suggest that a temporal gradient of Chinmo (Chinmo(high) {\textendash}\> Chinmo(low)) helps specify distinct birth order-dependent cell fates in an extended neuronal lineage.

}, keywords = {5{\textquoteright} Untranslated Regions, Amino Acid Sequence, Animals, Brain, Cell Differentiation, Cell Lineage, Developmental, Drosophila, Drosophila Proteins, Gene Expression Regulation, Larva, Molecular Sequence Data, Morphogenesis, Mushroom Bodies, Mutation, Nerve Tissue Proteins, Neurons, Post-Translational, Protein Processing, Time Factors, Transgenes, Zinc Fingers}, issn = {0092-8674}, doi = {10.1016/j.cell.2006.08.045}, author = {Zhu, Sijun and Lin, Suewei and Kao, Chih-Fei and Awasaki, Takeshi and Chiang, Ann-Shyn and Lee, Tzumin} }