paper.bib

@article{wu:2024, 
  title={Network state transitions during cortical development}, 
  ISSN={1471-003X}, 
  url={http://dx.doi.org/10.1038/s41583-024-00824-y}, 
  DOI={10.1038/s41583-024-00824-y}, 
  journal={Nature reviews. Neuroscience}, 
  author={Wu, Michelle W. and Kourdougli, Nazim and Portera-Cailliau, Carlos}, 
  year={2024}, 
  month=may, 
  language={en} }

@article{akin:2020, 
  title={Activity regulates brain development in the fly}, 
  volume={65}, 
  ISSN={0959-437X}, 
  DOI={10.1016/j.gde.2020.04.005},
  journal={Current opinion in genetics & development}, 
  publisher={Elsevier BV}, 
  author={Akin, Orkun and Zipursky, S. Lawrence}, 
  year={2020}, 
  month=dec, 
  pages={8–13}, 
  language={en} }

@article{ardiel:2022, 
  title={Stereotyped behavioral maturation and rhythmic quiescence in C. elegans embryos}, 
  volume={11}, 
  ISSN={2050-084X}, 
  url={http://dx.doi.org/10.7554/eLife.76836}, 
  DOI={10.7554/eLife.76836}, 
  journal={eLife}, 
  publisher={eLife Sciences Publications, Ltd}, 
  author={Ardiel, Evan L. and Lauziere, Andrew and Xu, Stephen and Harvey, Brandon J. and Christensen, Ryan Patrick and Nurrish, Stephen and Kaplan, Joshua M. and Shroff, Hari}, 
  year={2022}, 
  month=aug, 
  keywords={C. elegans; behavior; embryo; neuropeptides; neuroscience}, 
  language={en} }

@article{avasthi:2023, 
  title={Gotta catch ‘em all: Agar microchambers for high-throughput single-cell live imaging}, 
  ISSN={2998-4084}, 
  url={http://dx.doi.org/10.57844/arcadia-v1bg-6b60}, 
  DOI={10.57844/arcadia-v1bg-6b60}, 
  publisher={Arcadia Science}, 
  author={Avasthi, Prachee and Essock-Burns, Tara and Garcia, Galo, III and Gehring, Jase and Matus, David Q. and Mets, David G. and York, Ryan}, 
  year={2023}, 
  month=apr }

@article{blankenship:2009, 
  title={Mechanisms underlying spontaneous patterned activity in developing neural circuits}, 
  volume={11}, 
  ISSN={1471-003X}, 
  DOI={10.1038/nrn2759},
  number={1}, 
  journal={Nature reviews. Neuroscience}, 
  publisher={Nature Publishing Group}, 
  author={Blankenship, Aaron G. and Feller, Marla B.}, 
  year={2009}, 
  pages={18–29} }

@article{carreira:2021, 
  title={Mechanosensory input during circuit formation shapes Drosophila motor behavior through patterned spontaneous network activity}, 
  volume={31}, 
  ISSN={0960-9822}, 
  DOI={10.1016/j.cub.2021.08.022},
  number={23}, 
  journal={Current biology: CB}, 
  author={Carreira-Rosario, Arnaldo and York, Ryan A. and Choi, Minseung and Doe, Chris Q. and Clandinin, Thomas R.}, 
  year={2021}, 
  month=dec, 
  pages={5341–5349.e4}, 
  keywords={Drosophila embryo; behavioral development; development of locomotor behavior; nervous system development; neural circuit wiring; spontaneous network activity}, 
  language={en} }

@article{crisp:2008, 
  title={The development of motor coordination in Drosophila embryos}, 
  volume={3717}, 
  DOI={10.1242/dev.026773},
  author={Crisp, Sarah and Evers, Jan Felix and Fiala, André and Bate, Michael}, 
  year={2008}, 
  pages={3707–3717}, 
  keywords={coordination; drosophila; embryo; movement; muscle} }

@article{donoughe:2018, 
  title={High-throughput live-imaging of embryos in microwell arrays using a modular specimen mounting system}, 
  volume={7}, 
  ISSN={2046-6390}, 
  DOI={10.1242/bio.031260},
  number={7}, 
  journal={Biology open}, 
  publisher={The Company of Biologists}, 
  author={Donoughe, Seth and Kim, Chiyoung and Extavour, Cassandra G.}, 
  year={2018}, 
  month=jul, 
  pages={bio031260}, 
  keywords={Development; Embryogenesis; High-throughput; Image analysis; Microscopy; Quantitative imaging; Time lapse}, 
  language={en} }

@article{fischler:1981, 
  title={Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography}, 
  volume={24}, 
  ISSN={0001-0782}, 
  DOI={10.1145/358669.358692},
  number={6}, 
  journal={Communications of the ACM}, 
  publisher={Association for Computing Machinery (ACM)}, 
  author={Fischler, Martin A. and Bolles, Robert C.}, 
  year={1981}, 
  month=jun, 
  pages={381–395}, 
  language={en} }

@article{giovannucci:2019, 
  title={CaImAn an open source tool for scalable calcium imaging data analysis}, 
  volume={8}, 
  ISSN={2050-084X}, 
  url={http://dx.doi.org/10.7554/eLife.38173}, 
  DOI={10.7554/eLife.38173}, 
  journal={eLife}, 
  publisher={eLife Sciences Publications, Ltd}, 
  author={Giovannucci, Andrea and Friedrich, Johannes and Gunn, Pat and Kalfon, Jérémie and Brown, Brandon L. and Koay, Sue Ann and Taxidis, Jiannis and Najafi, Farzaneh and Gauthier, Jeffrey L. and Zhou, Pengcheng and Khakh, Baljit S. and Tank, David W. and Chklovskii, Dmitri B. and Pnevmatikakis, Eftychios A.}, 
  year={2019}, 
  month=jan, 
  keywords={calcium imaging; data analysis; mouse; neuroscience; one-photon; open source; software; two-photon; zebrafish}, 
  language={en} }

@article{lin:2016, 
  title={Genetically encoded indicators of neuronal activity}, 
  volume={19}, 
  ISSN={1097-6256}, 
  DOI={10.1038/nn.4359},
  number={9}, 
  journal={Nature neuroscience}, 
  publisher={Nature Publishing Group}, 
  author={Lin, Michael Z. and Schnitzer, Mark J.}, 
  year={2016}, 
  month=aug, 
  pages={1142–1153}, 
  language={en} }

@unpublished{menzies:2024, 
  title={A microRNA that controls the emergence of embryonic movement}, 
  url={http://dx.doi.org/10.7554/eLife.95209.2}, 
  DOI={10.7554/elife.95209.2}, 
  journal={eLife}, 
  author={Menzies, Jonathan A. C. and Chagas, Andre M. and Baden, Tom and Alonso, Claudio R.}, 
  year={2024}, 
  month=jun, 
  language={en} }

@article{nakai:2001, 
  title={A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein}, 
  volume={19}, 
  ISSN={1087-0156}, 
  DOI={10.1038/84397},
  number={2}, 
  journal={Nature biotechnology}, 
  publisher={Springer Science and Business Media LLC}, 
  author={Nakai, J. and Ohkura, M. and Imoto, K.}, 
  year={2001}, 
  month=feb, 
  pages={137–141}, 
  language={en} }

@article{otsu:1979, 
  title={A threshold selection method from gray-level histograms}, 
  volume={9}, 
  ISSN={0018-9472}, 
  DOI={10.1109/TSMC.1979.4310076},
  number={1}, 
  journal={IEEE transactions on systems, man, and cybernetics}, 
  publisher={Institute of Electrical and Electronics Engineers (IEEE)}, 
  author={Otsu, Nobuyuki}, 
  year={1979}, 
  month=jan, 
  pages={62–66}, 
  language={en} }

@unpublished{pachitariu:2016, 
  title={Suite2p: beyond 10,000 neurons with standard two-photon microscopy}, 
  url={https://www.biorxiv.org/content/10.1101/061507v2.abstract}, 
  DOI={10.1101/061507}, 
  journal={bioRxiv}, 
  publisher={bioRxiv}, 
  author={Pachitariu, Marius and Stringer, Carsen and Dipoppa, Mario and Schröder, Sylvia and Rossi, L. Federico and Dalgleish, Henry and Carandini, Matteo and Harris, Kenneth D.}, 
  year={2016}, 
  month=jun, 
  pages={061507}, 
  language={en} }

@article{virtanen:2020, 
  title={SciPy 1.0: fundamental algorithms for scientific computing in Python}, 
  volume={17}, 
  ISSN={1548-7091}, 
  DOI={10.1038/s41592-019-0686-2},
  number={3}, 
  journal={Nature methods}, 
  publisher={Springer Science and Business Media LLC}, 
  author={Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and Haberland, Matt and Reddy, Tyler and Cournapeau, David and Burovski, Evgeni and Peterson, Pearu and Weckesser, Warren and Bright, Jonathan and van der Walt, Stéfan J. and Brett, Matthew and Wilson, Joshua and Millman, K. Jarrod and Mayorov, Nikolay and Nelson, Andrew R. J. and Jones, Eric and Kern, Robert and Larson, Eric and Carey, C. J. and Polat, İlhan and Feng, Yu and Moore, Eric W. and VanderPlas, Jake and Laxalde, Denis and Perktold, Josef and Cimrman, Robert and Henriksen, Ian and Quintero, E. A. and Harris, Charles R. and Archibald, Anne M. and Ribeiro, Antônio H. and Pedregosa, Fabian and van Mulbregt, Paul and SciPy 1.0 Contributors}, 
  year={2020}, 
  month=mar, 
  pages={261–272}, 
  language={en} }