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Scientific Computing Software (HHMI Janelia)
เข้าร่วมเมื่อ 7 ก.พ. 2022
How To... Use repp to Facilitate Molecular Cloning
In this installment of the How To... interest group, Shaohe Wang and Christian Goina discuss Janelia's implementation of repp, a tool for planning Gibson Assembly experiments.
github.com/JaneliaSciComp/repp
shaohewanglab.org
github.com/JaneliaSciComp/repp
shaohewanglab.org
มุมมอง: 76
วีดีโอ
How to... use SNT to segment neurons
มุมมอง 242ปีที่แล้ว
In this meeting of Janelia's How To... interest group, Tiago Ferreira presents a hands-on overview of SNT.
How To... combine registered data to create an atlas
มุมมอง 71ปีที่แล้ว
How To... combine registered data to create an atlas
How to publish your data set (with or without a paper)
มุมมอง 75ปีที่แล้ว
In this installment of Janelia's How To... interest group, Virginia Scarlett shares practical tips about data publication (from a Janelia-centric perspective).
"Transformers in Natural Language Processing & Beyond" by Justin Joyce
มุมมอง 8Kปีที่แล้ว
Talk on 2023/07/18 by Justin Joyce at the Janelia Applied Deep Learning Interest Group. Covers fundamental architectures and an exploration of tools and services available. Slides: tinyurl.com/LLM-talk-slides
How To... Read and Write OME-NGFF Formatted Images
มุมมอง 110ปีที่แล้ว
In this meeting of Janelia's How To... interest group, John Bogovic and Virginia Scarlett discuss tools for working with OME-NGFF-formatted microscopy images.
How To... Register Your Data to an Atlas and Move Things Back and Forth
มุมมอง 294ปีที่แล้ว
In this installment of the How To... interest group, Greg Fleishman presents "How To... Register Your Data to an Atlas and Move Things Back and Forth" using BigStream.
VVDViewer: Multi-channels image adjustment
มุมมอง 280ปีที่แล้ว
The basic operation of 3D/4D rendering software: VVDViewer. github.com/JaneliaSciComp/VVDViewer The VVDViewer, an open-source software developed by the Janelia Research Campus (Scientific Computing Software), offers a user-friendly interface for volume visualization, segmentation, and analysis. In this movie, we delve into the VVDViewer's features and functions, including importing data, naviga...
"Practical Deep Learning" by Habib Bukhari
มุมมอง 316ปีที่แล้ว
Talk on 2023/05/23 by Habib Bukhari at the Janelia Applied Deep Learning Interest Group. Link to the 2nd place solution in the Kaggle IceCube Neutrino Detection Competition: github.com/DrHB/icecube-2nd-place
How to... work with json metadata using n5 and jq
มุมมอง 83ปีที่แล้ว
In this meeting of Janelia's How To... interest group, John Bogovic presents "How to... work with json metadata using n5 and jq". Recorded May 12, 2023.
How To... detect fluorescent spots in microscopy images using RS-FISH
มุมมอง 215ปีที่แล้ว
In this meeting of Janelia's How To... interest group, Stephan Preibisch presents "How To... detect fluorescent spots in microscopy images using RS-FISH". Recorded April 13, 2023.
How To... align huge microscopy images with Big Stitcher
มุมมอง 1.1Kปีที่แล้ว
In this meeting of Janelia's How To... Interest Group, Stephan Preibisch presents an overview of Big Stitcher. Recorded March 30, 2023.
Code review of Napari-ChatGPT by Loic Royer (CZI Biohub)
มุมมอง 745ปีที่แล้ว
For our regular code review sessions we recently had a visitor, Loic Royer from the CZI Biohub, who presented his Napari-ChatGPT project. It is also a nice introduction into how to use the Chat-GPT API for your own projects using langchain. github.com/royerlab/napari-chatgpt/ github.com/hwchase17/langchain/
Janelia Scientific Computing Software Overview (2023)
มุมมอง 260ปีที่แล้ว
Janelia Scientific Computing Software Overview (2023)
Sci Viz 2022-04-28: From Visual Analytics to Interactive Data Stories (Robert Krueger)
มุมมอง 2672 ปีที่แล้ว
Sci Viz 2022-04-28: From Visual Analytics to Interactive Data Stories (Robert Krueger)
Sci Viz 2022-05-12: Advanced Rendering Methods for Scientific Insight (John Stone)
มุมมอง 1342 ปีที่แล้ว
Sci Viz 2022-05-12: Advanced Rendering Methods for Scientific Insight (John Stone)
Sci Viz 2022-04-14: VisPy, Datoviz, PyGfx
มุมมอง 7762 ปีที่แล้ว
Sci Viz 2022-04-14: VisPy, Datoviz, PyGfx
How to ... Annotate using Paintera - Alyson Petruncio and Caleb Hulbert
มุมมอง 6372 ปีที่แล้ว
How to ... Annotate using Paintera - Alyson Petruncio and Caleb Hulbert
Sci Viz 2022-03-31: Neuroglancer (Jeremy Maitin-Shepard)
มุมมอง 4222 ปีที่แล้ว
Sci Viz 2022-03-31: Neuroglancer (Jeremy Maitin-Shepard)
How To... Manually Register Images with BigWarp - John Bogovic
มุมมอง 2.9K2 ปีที่แล้ว
How To... Manually Register Images with BigWarp - John Bogovic
How to... Get Started on the Janelia Compute Cluster - Rob Lines
มุมมอง 1072 ปีที่แล้ว
How to... Get Started on the Janelia Compute Cluster - Rob Lines
How to... Motion Correct Time Series Using Image Registration - Greg Fleishman
มุมมอง 2152 ปีที่แล้ว
How to... Motion Correct Time Series Using Image Registration - Greg Fleishman
Sci Viz 2022-03-03: Napari (Loic Royer)
มุมมอง 2462 ปีที่แล้ว
Sci Viz 2022-03-03: Napari (Loic Royer)
How to... run a DASK cluster easily - Greg Fleishman
มุมมอง 1422 ปีที่แล้ว
How to... run a DASK cluster easily - Greg Fleishman
Thanks for the nice presentations! Could you please get a better microfone :)
To your knowledge how well would this work for live neuronal cell cultures if we train the segmentation with cellpose 2.0? I have tried with 1.0 with mediocre results (~50% accuracy), and am wondering if I should put in the effort for the 2.0.
also i am using fluo 4 am
how can i do the unit test
Finally a tutorial that explains the dimensions! Thank you so much SIR!
The "hhmi" on the bottom of the slide. Is that Howard Hughes Medical Institute???
Yes :)
@@JaneliaSciComp The very first seconds of the video show "hhmi | Howard Hughes Medical Institute" on the upper left. I completely missed that. Now I feel silly.
thanks a lot 🙏❤
Awesome overview of the architecture and use cases! Thanks 🤩
Very interesting... Learned a lot of things I wouldn't normally run into.
Well explained👏👏
'promosm' 😚
To read the text in the Jupyter notebook clearly, make sure you are streaming the video with a high quality setting. Click the gear icon in the video player and make sure the quality setting is high enough.
Can you be more clear about VPN usage and obtaining a login?
Is it possible to register several stacks together? All stacks has a common image.
Yes you can, by giving BigWarp a multichannel image stack as your moving or fixed image. Then you'll be able to see all channels at once, and all moving images will be transformed at the same time. For a longer discussion consider posting on the forum (link in the description).
I have four fluorescent channels I am trying to register to each other. But I can only find a way to register two images at a time in Big Warp. Is there a way to align all four at once?
Running BigWarp once lets you produce one transformation, so you'll probably need to run it three times - assuming you pick one of your four channels as the fixed image and the three others need different transforms. For a longer discussion consider posting on the forum (link in the description).