Difference between revisions of "Workshops"

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developed by the Nemonic consortium.
 
developed by the Nemonic consortium.
  
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== 2020 Information ==
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==2023 Workshop==
  
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[[File:Flyer_nemonic_ws2_00.jpg|600px|center]]
 
  
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== 2019 Speakers ==
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[[File:Nemonic_draft.jpg|center]]
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==2022 Speakers==
  
 
<gallery widths=300px heights=200px mode="nolines">
 
<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:Jerome_Lecoq.jpg|Jérôme Lecoq, Allen Institute
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Image:Nico_Pegard.jpg|Nico Pegard, UNC Chapel Hill
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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
 
Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
 
Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
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Image:Emily_Gibson.jpg|Emily Gibson, UC Denver
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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/tHBeF2VNfL0|640|left}}
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{{#ev:youtube|https://youtu.be/63p3tHT6FI0|640|right}}
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{{#ev:youtube|https://youtu.be/rUwIqU6gVvw|640|left}}
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{{#ev:youtube|https://youtu.be/FZG1SMwf_CE|640|right}}
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{{#ev:youtube|https://youtu.be/ZGQgpG3ByYY|640|left}}
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{{#ev:youtube|https://youtu.be/OK-EKPIgKFQ|640|right}}
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{{#ev:youtube|https://youtu.be/eAwGQOiSOvE|640|left}}
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{{#ev:youtube|https://youtu.be/aZfpbt-31jw|640|right}}
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{{#ev:youtube|https://youtu.be/CJfCEegMmeQ|640|left}}
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{{#ev:youtube|https://youtu.be/72sT44Y4XZM|640|right}}
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<br clear=all>
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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 ==
 +
 
 +
<gallery widths=300px heights=200px mode="nolines">
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Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
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Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
 
Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
 
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:Darcy_Peterka.jpg|Darcy Peterka, Columbia
 +
Image:Kawasi.jpg|Kawasi Lett, Cornell
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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/z6TlH28MLRo|640|right}}
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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}}
  
 
<br clear=all>
 
<br clear=all>
  
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== 2019 Workshop Slideshows ==
 
  
−
[https://drive.google.com/file/d/1d51qP8bYEYDuoxELvALhJHYg8EkmXgPB/view?usp=sharing| Fast and scalable calcium imaging data analysis with CaImAn - Andrea Giovannucci]
+
==2021 Software Tutorials==
 +
 
 +
[https://github.com/UNC-optics/DeepCGH DeepCGH: 3D computer generated holography using deep learning - Nico Pegard]
 +
 
 +
[https://colab.research.google.com/drive/1vkp-uPV8tKavmX12bcN2L-jYH8_MgmHL?usp=sharing CaImAn’s Demo pipeline - Andrea Giovannucci]
 +
 
 +
[https://colab.research.google.com/drive/1m3ZZMqb2OMpRGXRStqqfmDxDRjlHevZT?usp=sharing Complete pipeline for online processing using CaImAn Online (OnACID) - Andrea Giovannucci]
 +
 
 +
[https://colab.research.google.com/drive/1F-GSVGXnL4MvoU7UyNAVTNeCAopugmwX?usp=sharing Demo pipeline for processing voltage imaging data - Andrea Giovannucci]
 +
 
 +
== 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
 +
Image:Rick.jpg|Rick Ayer, Sutter Instrument
 +
Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
 +
Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
 +
Image:Simon.jpg|Simon Schultz, Imperial College London
 +
Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
 +
 
 +
</gallery>
 +
 
 +
 
 +
 
 +
==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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<br clear=all>
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 +
 
 +
==2020 Workshop Slideshows==
 +
 
 +
[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]
 +
 
 +
[https://drive.google.com/file/d/1d65jhaoFW_MPfu-MVc6T8Qll35RUdudB/view?usp=sharing 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 ==
  
−
[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]
+
<gallery widths=300px heights=200px mode="nolines">
 +
Image:Kaspar_Podgorski.jpg|Kaspar Podgorski, Janelia Research Campus
 +
Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill
 +
Image:Darcy_Peterka.jpg|Darcy Peterka, Columbia
 +
Image:Emily_Gibson.jpg|Emily Gibson, CU Denver
 +
Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill
 +
Image:Simon.jpg|Simon Schultz, Imperial College London
 +
Image:Spencer_Smith_UCSB.jpg|Spencer Smith, UC Santa Barbara
  
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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]
+
</gallery>
  
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[https://drive.google.com/file/d/1yfxZpgaVVFpYPj7DnJU07u6mvcnCwACi/view?usp=sharing| High Speed Two-Photon Tomography - Kaspar Podgorski]
+
<br clear=all>
  
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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]
+
== 2019 Workshop Slideshows ==
  
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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]
+
[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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== 2019 Related Papers and Files==
+
[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]
  
−
CaImAn: an open source tool for scalable calcium imaging data analysis[https://elifesciences.org/articles/38173]
+
[https://drive.google.com/file/d/1jaftx6n5dvVkoM_oFKTdjJgI-QKQIgsC/view?usp=sharing Robotically automated, two-photon targeted patch clamp physiology - Simon Schultz]
  
−
Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology[https://www.sciencedirect.com/science/article/pii/S089662731730733X]
+
[https://drive.google.com/file/d/1yfxZpgaVVFpYPj7DnJU07u6mvcnCwACi/view?usp=sharing High Speed Two-Photon Tomography - Kaspar Podgorski]
  
−
Progress in automating patch clamp cellular physiology[https://journals.sagepub.com/doi/abs/10.1177/2398212818776561]
+
[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]
  
−
ABLE: An Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661356/]
+
[https://drive.google.com/file/d/1Cr_jK-VSmIBfMrZjOpeZcNOnEt5SqqZM/view?usp=sharing Darcy Peterka's 2019 Nemonic workshop talk - Darcy Peterka]
  
−
High speed functional imaging with source localized multifocal two-photon microscopy[https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-8-3678]
+
== 2019 Related Resources==
  
−
Building a two-photon microscope is easy[https://drive.google.com/file/d/1geiUITveydNTSxz2lFEHyazqjx9XdjUE/view?usp=sharing]
+
[https://elifesciences.org/articles/38173 CaImAn: an open source tool for scalable calcium imaging data analysis]
  
−
2019 Nemonic workshop schedule[https://drive.google.com/file/d/1lYX4XBZvLDpHrfMXJJIaZzYkoZC4xmuf/view?usp=sharing]
+
[https://www.sciencedirect.com/science/article/pii/S089662731730733X Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology]
  
−
== See Also ==
+
[https://journals.sagepub.com/doi/abs/10.1177/2398212818776561 Progress in automating patch clamp cellular physiology]
  
 +
[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5661356/ ABLE: An Activity-Based Level Set Segmentation Algorithm for Two-Photon Calcium Imaging Data]
  
 +
[https://www.osapublishing.org/boe/abstract.cfm?uri=boe-9-8-3678 High speed functional imaging with source localized multifocal two-photon microscopy]
  
 +
[https://drive.google.com/file/d/1geiUITveydNTSxz2lFEHyazqjx9XdjUE/view?usp=sharing Building a two-photon microscope is easy]
  
 +
== See Also ==
  
 +
[[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


Retrieved from "https://nemonic.ece.ucsb.edu/index.php?title=Workshops&oldid=607"