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we are incredibly happy to finally announce the release of Lead-DBS v3.0 which Ningfei just pushed to our servers! |
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A few points to note
Beyond a lot of methods updates, one major change of version 3 is that we switched to an entirely new data storage format which is based on the BIDS standard. This means that you will not be readily able to open up existing projects (from version 2) but will need to convert them to BIDS first. We put a lot of effort into this step (and had to cross some valleys to finally reach the hill). So we are confident that this conversion step works quite robustly by now. Still, it may make sense to:
- Consider finishing up projects in v.2 if they are close to completion
- Backup the data in the legacy format before upgrading to be on the safe side
- Check out the manual and tutorial to get accustomed to the new format before making the switch.
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Three data explorers finalized
Beyond the switch to BIDS, we are excited that the DBS sweetspot, fiberfiltering and network mapping explorers have evolved much further since their initial introduction and are officially the scientific / methodological centerpiece of version 3. |
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WarpDrive
Beyond the three new data explorers, Simon Oxenford's development of WarpDrive has created a real milestone in making Lead-DBS more accurate. Now officially released in v3.0, this tool allows you to manually refine normalization warpfields in order to i) better normalize patient images to standard space and ii) more accurately segment patient anatomy in native space. Especially if imaging quality is decent, it can be pure joy to work with WarpDrive. |
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WarpDrive in action: With this tool, definitions of subcortical nuclei become as good as the human eye. |
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OSS-DBS
Ever wondered whether more advanced bioelectrical modeling concepts such as pathway activation modeling could be carried out using open source tools? In 2020, Konstantin Butenko and Ursula van Rienen published the OSS-DBS toolbox, which has exactly this goal in mind. Together with Ningfei Li, Konstantin worked meticulously to create a symbiosis between OSS-DBS and Lead-DBS which could be dramatically sped up after Konstantin joined our lab in Boston. About three years later, we are excited to officially release the interface. As an aside, OSS-DBS 2.0 is already on the horizon, which has been developed with Lead-DBS in mind (and will be released soon). |
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New atlases
We included the following new subcortical atlases with Lead-DBS v3.0 and would like to take the opportunity to thank all colleagues that contributed their work to the toolbox: |
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Allen Brain Atlas (Ding 2020)
Alzheimer Response Network (Rios 2022)
Essential Tremor Probabilistic Mapping (Nowacki 2022)
PD Depression Network (Irmen 2020)
Probabilistic Thalamus Atlas (Iglesias 2018)
HCPex (Huang 2021)
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The Allan Brain Atlas – and yes, there are many subcortical structures below what can be seen. |
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Many a thank you
Creating version 3 was the most Herculanean effort we undertook as a lab – and as a community. It is impossible to thank everyone, but here is an attempt (in no particular order). If you feel unseen, please let us know but also please take our sincerest apologies. Creating this version took over 2 years, so we won't be able to thank everyone of you enough!
- Ningfei Li for overseeing the Lead-DBS development.
- Nanditha Rajamani for contributing by far the most after Ningfei, for complex features including multitract fiberfiltering and advanced stimulation detection algorithms.
- Konstantin Butenko for including OSS-DBS and a ton of code contributions to Lead-DBS beyond that.
- Simon Oxenford for creating WarpDrive, Lead-OR and lots of additional amazing tools inside the Lead-DBS Ecosphere.
- Garance Meyer for code contributions of the most complicated form (PCA based fiber filtering) & a huge amount of beta testing.
- Johannes Achtzehn for creating a beautiful DICOM import tool for Lead-DBS.
- Clemens Neudorfer for writing up the Lead-DBS v. 3 paper.
- Enrico Opri for very valuable discussions, bugfixing & code contributions.
- Till Dembek for incredible help & code in the DBS Sweetspot Explorer.
- Lauren Hart for tenacious testing of the BIDS import tool (among many others).
- Barbara Hollunder, Helen Friedrich & Lukas Goede for testing, testing, testing.
- Helen Friedrich, Barbara Hollunder & Ningfei Li for work on the new Lead-DBS logo.
- Aysu Sahin, Patricia Zvárova, Kavisha Fernando and Khoa Nguyen for updating the Lead-DBS manual.
- Greydon Gilmore & Jonathan Lau for valuable advice before moving to BIDS.
- Julian Neumann & Jonathan Vanhoecke for providing a great spirit when moving to BIDS.
- Johannes Achtzehn & Nanditha Rajamani for being the main drivers pushing us to move to BIDS.
- Konstantin Butenko for keeping up the spirit during BIDS import testing.
- Ningfei Li & Nanditha Rajamani for keeping their cool.
- Michael Loftus for code contributions & beta testing.
- Andreas Husch & Mehri Beniasadi for including Fastfield & DBSegment into Lead-DBS.
- Bassam Al-Fatly for being there for everyone, testing & support.
- Matteo Vissani & the Richardson Lab for testing & support.
- Ningfei Li, Simon Oxenford, Konstantin Butenko & Nanditha Rajamani for including a Conda Environment inside Lead-DBS (more on that later).
- Ningfei Li for updating binaries so often & continuously making sure they work on all 3 operating systems.
- Melissa Chua & Jordy Tasserie for bug reporting & beta testing.
- A big THANK YOU to countless contributors of data & atlases (who are of course mentioned on website & inside of Lead-DBS by citation)
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Save the date: OptoDBS 2024!
OptoDBS will return as likely the most mechanistic DBS (and optogenetics) conference in Geneva from June 12-14 2024.
OptoDBS is a unique conference with a mechanistic focus and aims at juxtaposing findings from the DBS world with similar topics from the optogenetics world.
We are still working on the program and speaker invitations but are already very excited about the preliminary concept of next years conference and look forward to seeing some of you in Geneva! |
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Christian & I talk about the philosophy behind the conference in form of a stimulating brains podcast episode. Tune in here! |
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As always, feel free to connect with us via Twitter or Slack.
…or fork/meet us on github to contribute directly!
Did you know? You are one of 7412 dear colleagues on our mailing list.
Thank you so much for your ongoing support!
Best regards on behalf of the Lead-DBS team,
Andy |
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