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CAVE: Connectome Annotation Versioning Engine.
Dorkenwald S, Schneider-Mizell CM, Brittain D, Halageri A, Jordan C, Kemnitz N, Castro MA, Silversmith W, Maitin-Shephard J, Troidl J, Pfister H, Gillet V, Xenes D, Bae JA, Bodor AL, Buchanan J, Bumbarger DJ, Elabbady L, Jia Z, Kapner D, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Reid RC, da Costa NM, Seung HS, Collman F. Dorkenwald S, et al. Among authors: mondal ss. bioRxiv [Preprint]. 2023 Jul 28:2023.07.26.550598. doi: 10.1101/2023.07.26.550598. bioRxiv. 2023. Update in: Nat Methods. 2025 May;22(5):1112-1120. doi: 10.1038/s41592-024-02426-z. PMID: 37546753 Free PMC article. Updated. Preprint.
Connectomics of predicted Sst transcriptomic types in mouse visual cortex.
Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Joyce E, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu SC, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA. Gamlin CR, et al. Among authors: mondal ss. Nature. 2025 Apr;640(8058):497-505. doi: 10.1038/s41586-025-08805-6. Epub 2025 Apr 9. Nature. 2025. PMID: 40205210 Free PMC article.
Inhibitory specificity from a connectomic census of mouse visual cortex.
Schneider-Mizell CM, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Elabbady L, Gamlin C, Kapner D, Kinn S, Mahalingam G, Seshamani S, Suckow S, Takeno M, Torres R, Yin W, Dorkenwald S, Bae JA, Castro MA, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Reimer J, Tolias AS, Seung HS, Reid RC, Collman F, da Costa NM. Schneider-Mizell CM, et al. Among authors: mondal ss. Nature. 2025 Apr;640(8058):448-458. doi: 10.1038/s41586-024-07780-8. Epub 2025 Apr 9. Nature. 2025. PMID: 40205209 Free PMC article.
Loss of Stim2 in zebrafish induces glaucoma-like phenotype.
Baranykova S, Gupta RK, Kajdasz A, Wasilewska I, Macias M, Szybinska A, Węgierski T, Nahia KA, Mondal SS, Winata CL, Kuźnicki J, Majewski L. Baranykova S, et al. Among authors: mondal ss. Sci Rep. 2024 Oct 18;14(1):24442. doi: 10.1038/s41598-024-74909-0. Sci Rep. 2024. PMID: 39424970 Free PMC article.
Functional connectomics reveals general wiring rule in mouse visual cortex.
Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Chang A, Kunin AB, Tran D, Fu J, Ding Z, Patel S, Ntanavara L, Froebe R, Ponder K, Muhammad T, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Yatsenko D, Froudarakis E, Sinz F, Josić K, Rosenbaum R, Seung HS, Collman F, da Costa NM, Reid RC, Walker EY, Pitkow X, Reimer J, Tolias AS. Ding Z, et al. Among authors: mondal ss. Nature. 2025 Apr;640(8058):459-469. doi: 10.1038/s41586-025-08840-3. Epub 2025 Apr 9. Nature. 2025. PMID: 40205211 Free PMC article.
Perisomatic ultrastructure efficiently classifies cells in mouse cortex.
Elabbady L, Seshamani S, Mu S, Mahalingam G, Schneider-Mizell CM, Bodor AL, Bae JA, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Nehoran B, Popovych S, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Seung HS, Reid RC, da Costa NM, Collman F. Elabbady L, et al. Among authors: mondal ss. Nature. 2025 Apr;640(8058):478-486. doi: 10.1038/s41586-024-07765-7. Epub 2025 Apr 9. Nature. 2025. PMID: 40205216 Free PMC article.
NEURD offers automated proofreading and feature extraction for connectomics.
Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E, Papadopoulos C, Kunin AB, Patel S, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yu SC, Yin W, Xenes D, Kitchell LM, Rivlin PK, Rose VA, Bishop CA, Wester B, Froudarakis E, Walker EY, Sinz F, Seung HS, Collman F, da Costa NM, Reid RC, Pitkow X, Tolias AS, Reimer J. Celii B, et al. Among authors: mondal ss. Nature. 2025 Apr;640(8058):487-496. doi: 10.1038/s41586-025-08660-5. Epub 2025 Apr 9. Nature. 2025. PMID: 40205208 Free PMC article.
CAVE: Connectome Annotation Versioning Engine.
Dorkenwald S, Schneider-Mizell CM, Brittain D, Halageri A, Jordan C, Kemnitz N, Castro MA, Silversmith W, Maitin-Shephard J, Troidl J, Pfister H, Gillet V, Xenes D, Bae JA, Bodor AL, Buchanan J, Bumbarger DJ, Elabbady L, Jia Z, Kapner D, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Reid RC, da Costa NM, Seung HS, Collman F. Dorkenwald S, et al. Among authors: mondal ss. Nat Methods. 2025 May;22(5):1112-1120. doi: 10.1038/s41592-024-02426-z. Epub 2025 Apr 9. Nat Methods. 2025. PMID: 40205066 Free PMC article.
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex.
Bodor AL, Schneider-Mizell CM, Zhang C, Elabbady L, Mallen A, Bergeson A, Brittain D, Buchanan J, Bumbarger DJ, Dalley R, Gamlin C, Joyce E, Kapner D, Kinn S, Mahalingam G, Seshamani S, Suckow S, Takeno M, Torres R, Yin W, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Yu SC, Wong W, Wu J, Celii B, Campagnola L, Seeman SC, Jarsky T, Ren N, Arkhipov A, Reimer J, Seung HS, Reid RC, Collman F, da Costa NM. Bodor AL, et al. Among authors: mondal ss. Nat Neurosci. 2025 Aug;28(8):1704-1715. doi: 10.1038/s41593-025-02004-2. Epub 2025 Jul 28. Nat Neurosci. 2025. PMID: 40721677 Free PMC article.
53 results