Difference between revisions of "Workshops"
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developed by the Nemonic consortium. | developed by the Nemonic consortium. | ||
− | = 2022 Speakers == | + | ==2023 Workshop== |
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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"> | ||
− | Image:Jerome_Lecoq. | + | Image:Jerome_Lecoq.jpg|Jérôme Lecoq, Allen Institute |
− | + | Image:Xin_Ye.jpg|Xin Ye, BU | |
Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill | Image:Andrea.png|Andrea Giovannucci, UNC Chapel Hill | ||
Image:Kaspar_Podgorski.jpg|Kaspar Podgorski, Allen Institute | Image:Kaspar_Podgorski.jpg|Kaspar Podgorski, Allen Institute | ||
Image:Simon.jpg|Simon Schultz, Imperial College London | Image:Simon.jpg|Simon Schultz, Imperial College London | ||
Image:Emily_Gibson.jpg|Emily Gibson, CU Denver | Image:Emily_Gibson.jpg|Emily Gibson, CU Denver | ||
− | Image:Bruno_Pichler|Bruno Pichler, INSS | + | Image:Bruno_Pichler.jpg|Bruno Pichler, INSS |
Image:Kawasi.jpg|Kawasi Lett, Cornell | Image:Kawasi.jpg|Kawasi Lett, Cornell | ||
Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill | Image:Nico_Pegard.jpg|Nico Pégard, UNC Chapel Hill | ||
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==2022 Software Tutorials== | ==2022 Software Tutorials== | ||
− | [https://github.com/AllenInstitute/deepinterpolation/blob/master/examples/GoogleColab_example_Ophys__Finetuning_and_Inference_Workshop.ipynb | + | [https://github.com/AllenInstitute/deepinterpolation/blob/master/examples/GoogleColab_example_Ophys__Finetuning_and_Inference_Workshop.ipynb Ophys Finetuning and Inference - Jérôme Lecoq] |
− | [https://github.com/UNC-optics/Introduction-to-holography | + | [https://github.com/UNC-optics/Introduction-to-holography Introduction to Holography - Nico Pégard] |
− | [https://github.com/UNC-optics/DeepCGH | + | [https://github.com/UNC-optics/DeepCGH Deep CGH GitHub - Nico Pégard] |
− | [https://colab.research.google.com/drive/1s9zPDb6TArwB4FSUBiUBIuVr9SdtrXnM?usp=sharing | + | [https://colab.research.google.com/drive/1s9zPDb6TArwB4FSUBiUBIuVr9SdtrXnM?usp=sharing DeepCGH: 3D computer generated holography using deep learning - Nico Pégard] |
− | [https://colab.research.google.com/drive/1vkp-uPV8tKavmX12bcN2L-jYH8_MgmHL?usp=sharing | + | [https://colab.research.google.com/drive/1vkp-uPV8tKavmX12bcN2L-jYH8_MgmHL?usp=sharing CaImAn’s Demo pipeline - Andrea Giovannucci] |
− | [https://github.com/flatironinstitute/CaImAn | + | [https://github.com/flatironinstitute/CaImAn CaImAn GitHub - Andrea Giovannucci] |
== 2021 Speakers == | == 2021 Speakers == | ||
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[https://github.com/UNC-optics/DeepCGH DeepCGH: 3D computer generated holography using deep learning - Nico Pegard] | [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 | + | [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 | + | [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 | + | [https://colab.research.google.com/drive/1F-GSVGXnL4MvoU7UyNAVTNeCAopugmwX?usp=sharing Demo pipeline for processing voltage imaging data - Andrea Giovannucci] |
== 2020 Speakers == | == 2020 Speakers == | ||
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==2020 Workshop Slideshows== | ==2020 Workshop Slideshows== | ||
− | [https://www.dropbox.com/s/lw5zpzhuvtb0y7k/Schultz%20slides%20Neuronex%202020.pdf?dl=0 | + | [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] |
− | [https://drive.google.com/file/d/1SOMoVpL8QR2k_om3BXadlJlyT3lIdbMg/view?usp=sharing | + | [https://drive.google.com/file/d/1SOMoVpL8QR2k_om3BXadlJlyT3lIdbMg/view?usp=sharing Open Platforms for Two- and Three-Photon Microscopy - Rick Ayer] |
− | [https://www.dropbox.com/s/09s1gnf89cm90pb/2020_02_26_Nemonic%20copy.key?dl=0 | + | [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] |
− | [https://www.dropbox.com/s/63lvmxaiwjmk8wh/Nemonic%20Seminar.pptx?dl=0 | + | [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 | + | [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== | ==2020 Related Resources== | ||
Line 188: | Line 193: | ||
== 2019 Workshop Slideshows == | == 2019 Workshop Slideshows == | ||
− | [https://drive.google.com/file/d/1d51qP8bYEYDuoxELvALhJHYg8EkmXgPB/view?usp=sharing | + | [https://drive.google.com/file/d/1d51qP8bYEYDuoxELvALhJHYg8EkmXgPB/view?usp=sharing Fast and scalable calcium imaging data analysis with CaImAn - Andrea Giovannucci] |
− | [https://drive.google.com/file/d/1ODxntA7qm54joT4Pebk6pZisuBVyeFdV/view?usp=sharing | + | [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] |
− | [https://drive.google.com/file/d/1jaftx6n5dvVkoM_oFKTdjJgI-QKQIgsC/view?usp=sharing | + | [https://drive.google.com/file/d/1jaftx6n5dvVkoM_oFKTdjJgI-QKQIgsC/view?usp=sharing Robotically automated, two-photon targeted patch clamp physiology - Simon Schultz] |
− | [https://drive.google.com/file/d/1yfxZpgaVVFpYPj7DnJU07u6mvcnCwACi/view?usp=sharing | + | [https://drive.google.com/file/d/1yfxZpgaVVFpYPj7DnJU07u6mvcnCwACi/view?usp=sharing High Speed Two-Photon Tomography - Kaspar Podgorski] |
− | [https://drive.google.com/file/d/17bMJbctNsF2DQNLSYF__1R5aKk-s7G4O/view?usp=sharing | + | [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] |
− | [https://drive.google.com/file/d/1Cr_jK-VSmIBfMrZjOpeZcNOnEt5SqqZM/view?usp=sharing | + | [https://drive.google.com/file/d/1Cr_jK-VSmIBfMrZjOpeZcNOnEt5SqqZM/view?usp=sharing Darcy Peterka's 2019 Nemonic workshop talk - Darcy Peterka] |
== 2019 Related Resources== | == 2019 Related Resources== | ||
− | CaImAn: an open source tool for scalable calcium imaging data analysis | + | [https://elifesciences.org/articles/38173 CaImAn: an open source tool for scalable calcium imaging data analysis] |
− | + | [https://www.sciencedirect.com/science/article/pii/S089662731730733X Robotic Automation of In Vivo Two-Photon Targeted Whole-Cell Patch-Clamp Electrophysiology] | |
− | + | [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 == | == See Also == |
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.
Contents
2023 Workshop
2022 Speakers
2022 Videos
2022 Software Tutorials
Ophys Finetuning and Inference - Jérôme Lecoq
Introduction to Holography - Nico Pégard
DeepCGH: 3D computer generated holography using deep learning - Nico Pégard
CaImAn’s Demo pipeline - Andrea Giovannucci
CaImAn GitHub - Andrea Giovannucci
2021 Speakers
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
2020 Videos
2020 Workshop Slideshows
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
2019 Workshop Slideshows
Fast and scalable calcium imaging data analysis with CaImAn - Andrea Giovannucci
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