Difference between revisions of "Workshops"

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[[File:Logo_work_nemonic_01.jpg|thumb|300px]]
 
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The goal of the '''Nemonic Project''' ('''Ne'''xt generation '''M'''ultiph'''o'''ton '''N'''euro'''i'''maging '''C'''onsortium) is to develop and widely disseminate state-of-the-art technology for multiphoton imaging and associated techniques to the neuroscience community, and to advance emerging technology for future innovation in multiphoton neuroimaging. Ultimately, the activities of the Nemonic project will enable new experiments and accelerate discoveries in neuroscience.
 
  
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The Nemonic project holds a yearly workshops at UC Santa Barbara to help train
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personnel from other institutions on how to create and use novel multiphoton neuroimaging instrumentation
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developed by the Nemonic consortium.
  
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== Project Overview ==
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==2023 Workshop==
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The Nemonic project has three parts. First, there is a development component, called DEV, to create new technology to overcome critical barrier to progress in neuroscience. In a series of Case Studies, neuroengineers will develop custom instrumentation to enable currently impossible neuroscience experiments. A proven work flow involving custom optics and iterative refinement, and culminating in commercially produced parts, will be used to create the custom instrumentation. The Case Studies involve a range of animal models (mice, ferrets, cats, and monkeys), and optical and instrumental challenges.
 
  
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Second, there is a dissemination component, called DISSEM, to spread this technology broadly to other labs. All engineering materials and resources generated in the Case Studies will be open-sourced and released to the broader public in thoroughly documented and curated web resource. Components and systems developed in the Case Studies will be made commercially available. Also, a series of workshops are held to train scientists on how to design and build custom systems for multiphoton neuroimaging.
 
  
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Third, there is an advancement component, called ADV, to push the technology of multiphoton neuroimaging into the next frontier. Two technologies will be pursued: miniaturized, highly integrated photonic systems for practical and scalable head-mounted multiphoton neuroimaging in freely moving animals; and superresolution imaging to resolve structures relevant to synaptic and molecular dynamics in vivo. A series of meetings with top names in the field are held to promote novel collaborations and more rapidly advance technologies that are relevant to multiphoton neuroimaging in the future.
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[[File:Nemonic_draft.jpg|center]]
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==2022 Speakers==
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<gallery widths=300px heights=200px mode="nolines">
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Image:Jerome_Lecoq.jpg|Jérôme Lecoq, Allen Institute
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Image:Xin_Ye.jpg|Xin Ye, BU
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Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
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Image:Kaspar_Podgorski.jpg|Kaspar Podgorski, Allen Institute
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Image:Simon.jpg|Simon Schultz, Imperial College London
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Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
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Image:Bruno_Pichler.jpg|Bruno Pichler, INSS
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Image:Kawasi.jpg|Kawasi Lett, Cornell
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Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
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Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
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Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
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</gallery>
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==2022 Videos==
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{{#ev:youtube|https://youtu.be/eAwGQOiSOvE|640|left}}
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For a more in depth description go to [[Project Details]]
 
 
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== Speakers ==
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==2022 Software Tutorials==
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[https://github.com/AllenInstitute/deepinterpolation/blob/master/examples/GoogleColab_example_Ophys__Finetuning_and_Inference_Workshop.ipynb Ophys Finetuning and Inference - Jérôme Lecoq]
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[https://github.com/UNC-optics/Introduction-to-holography Introduction to Holography - Nico Pégard]
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[https://github.com/UNC-optics/DeepCGH Deep CGH GitHub - Nico Pégard]
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[https://colab.research.google.com/drive/1s9zPDb6TArwB4FSUBiUBIuVr9SdtrXnM?usp=sharing DeepCGH: 3D computer generated holography using deep learning - Nico Pégard]
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[https://colab.research.google.com/drive/1vkp-uPV8tKavmX12bcN2L-jYH8_MgmHL?usp=sharing CaImAn’s Demo pipeline - Andrea Giovannucci]
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[https://github.com/flatironinstitute/CaImAn CaImAn GitHub - Andrea Giovannucci]
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== 2021 Speakers ==
  
 
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Image:Spencer_Smith_UCSB.jpg|Kaspar Podgorski Janelia Research Campus
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Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
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Image:John_Bowers_UCSB.jpg|Nico Pegard UNC Chapel Hill
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Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
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Image:Jerry_Chen_BU.jpg|Darcy Peterka Columbia
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Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
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Image:Michael_Goard_UCSB.jpg|Emily Gibson UC Denver
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Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
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Image:Andrea.png|Andrea Giovannucci UNC Chapel Hill
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Image:Kawasi.jpg|Kawasi Lett, Cornell
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Image:Kristina_Nielsen_JHU.jpg|Simon Schultz Imperial college London
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Image:Bruce.jpg|Bruce Kimmel, Vidrio Technologies
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Image:Adam.jpg|Adam Heiniger, TOPTICA
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Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
  
 
</gallery>
 
</gallery>
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==2021 Videos==
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{{#ev:youtube|https://youtu.be/840N69iuL2g|640|left}}
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{{#ev:youtube|https://youtu.be/rFyFsfgNa3Q|640|right}}
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{{#ev:youtube|https://youtu.be/NZZ6_zo0YIM|640|left}}
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{{#ev:youtube|https://youtu.be/J1z4MIerAZ0|640|left}}
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{{#ev:youtube|https://youtu.be/SKou5Watip4|640|right}}
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{{#ev:youtube|https://youtu.be/4UHRRKJhp_Y|640|left}}
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{{#ev:youtube|https://youtu.be/tiCPBUMHFoE|640|right}}
  
 
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== Funding ==
 
  
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The Nemonic project is funded through a National Science Foundation [https://neuronex.org/about NeuroNex] (Next Generation Networks for Neuroscience) award.
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==2021 Software Tutorials==
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[https://github.com/UNC-optics/DeepCGH DeepCGH: 3D computer generated holography using deep learning - Nico Pegard]
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[https://colab.research.google.com/drive/1vkp-uPV8tKavmX12bcN2L-jYH8_MgmHL?usp=sharing CaImAn’s Demo pipeline - Andrea Giovannucci]
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[https://colab.research.google.com/drive/1m3ZZMqb2OMpRGXRStqqfmDxDRjlHevZT?usp=sharing Complete pipeline for online processing using CaImAn Online (OnACID) - Andrea Giovannucci]
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[https://colab.research.google.com/drive/1F-GSVGXnL4MvoU7UyNAVTNeCAopugmwX?usp=sharing Demo pipeline for processing voltage imaging data - Andrea Giovannucci]
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== 2020 Speakers ==
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<gallery widths=300px heights=200px mode="nolines">
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Image:Jeff_Squier_CSM.jpg|Jeff Squier, Colorado School of Mines
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Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
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Image:Rick.jpg|Rick Ayer, Sutter Instrument
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Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
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Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
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Image:Simon.jpg|Simon Schultz, Imperial College London
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Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
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</gallery>
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==2020 Videos==
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{{#ev:youtube|https://youtu.be/KjHrjhvhRy0|640|left}}
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{{#ev:youtube|https://youtu.be/JAA89HQRaLw|640|right}}
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{{#ev:youtube|https://youtu.be/AT6cIu-hmcc|640|left}}
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{{#ev:youtube|https://youtu.be/S8wy6dARktk|640|right}}
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{{#ev:youtube|https://youtu.be/UNSTEdjJZEU|640|left}}
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{{#ev:youtube|https://youtu.be/GImZdKUwvuc|640|right}}
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==2020 Workshop Slideshows==
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[https://www.dropbox.com/s/lw5zpzhuvtb0y7k/Schultz%20slides%20Neuronex%202020.pdf?dl=0 Multiphoton imaging of hippocampal place cell network activity in mouse models of neurodegenerative disease - Simon Schultz]
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[https://drive.google.com/file/d/1SOMoVpL8QR2k_om3BXadlJlyT3lIdbMg/view?usp=sharing Open Platforms for Two- and Three-Photon Microscopy - Rick Ayer]
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[https://www.dropbox.com/s/09s1gnf89cm90pb/2020_02_26_Nemonic%20copy.key?dl=0 Fast and scalable brain imaging data at single-cell resolution - Andrea Giovannucci]
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[https://www.dropbox.com/s/63lvmxaiwjmk8wh/Nemonic%20Seminar.pptx?dl=0 3D-SHOT with Computer Generated Holography at high speed and with high performance - Nicolas Pegard]
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[https://drive.google.com/file/d/1d65jhaoFW_MPfu-MVc6T8Qll35RUdudB/view?usp=sharing Advances in two-dimensional spatial frequency modulation imaging - Jeff Squier]
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==2020 Related Resources==
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https://www.youtube.com/watch?v=DLTaqzz8hJM&feature=youtu.be
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== 2019 Speakers ==
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<gallery widths=300px heights=200px mode="nolines">
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Image:Kaspar_Podgorski.jpg|Kaspar Podgorski, Janelia Research Campus
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Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
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Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
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Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
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Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
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Image:Simon.jpg|Simon Schultz, Imperial College London
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Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
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</gallery>
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<br clear=all>
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== 2019 Workshop Slideshows ==
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[https://drive.google.com/file/d/1d51qP8bYEYDuoxELvALhJHYg8EkmXgPB/view?usp=sharing Fast and scalable calcium imaging data analysis with CaImAn - Andrea Giovannucci]
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[https://drive.google.com/file/d/1ODxntA7qm54joT4Pebk6pZisuBVyeFdV/view?usp=sharing From Holography to 3D-SHOT Multiphoton whole-cell photostimulation in 3D With single neuron resolution and millisecond precision - Nico Pegard]
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[https://drive.google.com/file/d/1jaftx6n5dvVkoM_oFKTdjJgI-QKQIgsC/view?usp=sharing Robotically automated, two-photon targeted patch clamp physiology - Simon Schultz]
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[https://drive.google.com/file/d/1yfxZpgaVVFpYPj7DnJU07u6mvcnCwACi/view?usp=sharing High Speed Two-Photon Tomography - Kaspar Podgorski]
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[https://drive.google.com/file/d/17bMJbctNsF2DQNLSYF__1R5aKk-s7G4O/view?usp=sharing Extending multiphoton microscopy to 3D brain imaging in freely moving mice - Emily Gibson]
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[https://drive.google.com/file/d/1Cr_jK-VSmIBfMrZjOpeZcNOnEt5SqqZM/view?usp=sharing Darcy Peterka's 2019 Nemonic workshop talk - Darcy Peterka]
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== 2019 Related Resources==
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[https://elifesciences.org/articles/38173 CaImAn: an open source tool for scalable calcium imaging data analysis]
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[https://www.sciencedirect.com/science/article/pii/S089662731730733X Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology]
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[https://journals.sagepub.com/doi/abs/10.1177/2398212818776561 Progress in automating patch clamp cellular physiology]
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[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661356/ ABLE: An Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data]
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[https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-8-3678 High speed functional imaging with source localized multifocal two-photon microscopy]
  
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== See Also==
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[https://drive.google.com/file/d/1geiUITveydNTSxz2lFEHyazqjx9XdjUE/view?usp=sharing Building a two-photon microscope is easy]
  
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Visit our discussion board to talk and ask questions! [https://nemonic.ece.ucsb.edu/board/ Discussion Board]
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== See Also ==
  
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[[Big Brain]]
  
 
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Latest revision as of 17:48, 20 February 2023


The Nemonic project holds a yearly workshops at UC Santa Barbara to help train personnel from other institutions on how to create and use novel multiphoton neuroimaging instrumentation developed by the Nemonic consortium.

2023 Workshop

Nemonic draft.jpg

2022 Speakers

  • Jérôme Lecoq, Allen Institute

  • Xin Ye, BU

  • Andrea Giovannucci, UNC Chapel Hill

  • Kaspar Podgorski, Allen Institute

  • Simon Schultz, Imperial College London

  • Emily Gibson, CU Denver

  • Bruno Pichler, INSS

  • Kawasi Lett, Cornell

  • Nico Pégard, UNC Chapel Hill

  • Darcy Peterka, Columbia

  • Spencer Smith, UC Santa Barbara

2022 Videos








2022 Software Tutorials

Ophys Finetuning and Inference - Jérôme Lecoq

Introduction to Holography - Nico Pégard

Deep CGH GitHub - Nico Pégard

DeepCGH: 3D computer generated holography using deep learning - Nico Pégard

CaImAn’s Demo pipeline - Andrea Giovannucci

CaImAn GitHub - Andrea Giovannucci

2021 Speakers

  • Nico Pégard, UNC Chapel Hill

  • Emily Gibson, CU Denver

  • Andrea Giovannucci, UNC Chapel Hill

  • Darcy Peterka, Columbia

  • Kawasi Lett, Cornell

  • Bruce Kimmel, Vidrio Technologies

  • Adam Heiniger, TOPTICA

  • Spencer Smith, UC Santa Barbara

2021 Videos






2021 Software Tutorials

DeepCGH: 3D computer generated holography using deep learning - Nico Pegard

CaImAn’s Demo pipeline - Andrea Giovannucci

Complete pipeline for online processing using CaImAn Online (OnACID) - Andrea Giovannucci

Demo pipeline for processing voltage imaging data - Andrea Giovannucci

2020 Speakers

  • Jeff Squier, Colorado School of Mines

  • Nico Pégard, UNC Chapel Hill

  • Rick Ayer, Sutter Instrument

  • Emily Gibson, CU Denver

  • Andrea Giovannucci, UNC Chapel Hill

  • Simon Schultz, Imperial College London

  • Spencer Smith, UC Santa Barbara


2020 Videos





2020 Workshop Slideshows

Multiphoton imaging of hippocampal place cell network activity in mouse models of neurodegenerative disease - Simon Schultz

Open Platforms for Two- and Three-Photon Microscopy - Rick Ayer

Fast and scalable brain imaging data at single-cell resolution - Andrea Giovannucci

3D-SHOT with Computer Generated Holography at high speed and with high performance - Nicolas Pegard

Advances in two-dimensional spatial frequency modulation imaging - Jeff Squier

2020 Related Resources

https://www.youtube.com/watch?v=DLTaqzz8hJM&feature=youtu.be

2019 Speakers

  • Kaspar Podgorski, Janelia Research Campus

  • Nico Pégard, UNC Chapel Hill

  • Darcy Peterka, Columbia

  • Emily Gibson, CU Denver

  • Andrea Giovannucci, UNC Chapel Hill

  • Simon Schultz, Imperial College London

  • Spencer Smith, UC Santa Barbara


2019 Workshop Slideshows

Fast and scalable calcium imaging data analysis with CaImAn - Andrea Giovannucci

From Holography to 3D-SHOT Multiphoton whole-cell photostimulation in 3D With single neuron resolution and millisecond precision - Nico Pegard

Robotically automated, two-photon targeted patch clamp physiology - Simon Schultz

High Speed Two-Photon Tomography - Kaspar Podgorski

Extending multiphoton microscopy to 3D brain imaging in freely moving mice - Emily Gibson

Darcy Peterka's 2019 Nemonic workshop talk - Darcy Peterka

2019 Related Resources

CaImAn: an open source tool for scalable calcium imaging data analysis

Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology

Progress in automating patch clamp cellular physiology

ABLE: An Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data

High speed functional imaging with source localized multifocal two-photon microscopy

Building a two-photon microscope is easy

See Also

Big Brain


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