diff --git a/assets/jupyter/blog.ipynb.html b/assets/jupyter/blog.ipynb.html index 7fc0370659b5..b7c716020743 100644 --- a/assets/jupyter/blog.ipynb.html +++ b/assets/jupyter/blog.ipynb.html @@ -1,4 +1,4 @@ - jekyll-jupyter-notebook20240410-1892-wxxfun \ No newline at end of file + lab values | Nolan & Sürmeli Labs

lab values

This document is inspired by Mariam Aly’s excellent article. This page contains brief information about the lab goals, expectations and responsibilities and publication policies. An expanded version of this document and additional practical information about mailing lists, calendars, contact numbers, computing resources, animal management and experimental protocols is on our internal wiki.

Goals

We aim to do the best science we can with the resources available to us. We are committed to supporting creative and rigorous science that aims to address important questions, and to making the process enjoyable and rewarding for everyone involved. We expect everyone in our labs to share this commitment.

Expectations and responsibilities

With help from current and previous lab members we’ve put together below principles and general expectations for everyone, for ourselves, for postdocs and PhD students, for lab staff and for undergraduates. An expanded version of this document is available on the wiki.

Everyone

We’re lucky to be surrounded by talented colleagues from diverse backgrounds. Our expectation is that everyone will contribute to a respectful, open, positive and productive work environment.

Gülşen and Matt

We aim to ensure our labs carry out rigorous science that addresses important research questions, to support students and staff in our labs in their personal and career development, and to provide a respectful and supportive environment for everyone in our labs. We encourage everyone to maintain a healthy work-life balance, take holidays and pay attention to long-term career development as well as immediately project goals.

Postdocs, research staff and PhD students

Postdocs and PhD students should expect to lead projects addressing questions within the big picture goals of the Sürmeli and Nolan labs; we encourage collaboration and co-leads where this helps address an important goal. We expect research staff to play important roles contributing to the delivery of research projects. We hope that you will take opportunities to contribute collaboratively to other lab projects and to training of junior lab members, and we expect you to make the our labs a collaborative and intellectually engaging environment.

Masters and undergraduate students

We strongly encourage you to take advantage of your time in the lab to learn from other people about what they are doing. You will usually work with a postdoc or PhD student on a specific question as part of a larger project. This person will provide you with lab training needed to address your project goals

Publication policies

Preprints and journals

We aim to share all manuscripts as preprints before submitting to a journal. Which journals to submit to is a joint decision between first and lead author(s). Our preference is to submit to non-profit journals with a strong commitment to open science (e.g. eLife). We recognise that scientific job and funding evaluation is far from perfect and will submit elsewhere if the first author(s) prefer.

Data and code

We aim to share all data and code, see data & code.

Authorship

We support use of the CRedIT taxonomy for documenting author contributions to research papers.Qualificaton for authorship requires meeting at least one of the CRedIT criteria. In determining position on authorship lists we follow the convention that the first author(s) have usually carried out most of the key experiments and provide strong intellectual drive, the senior authors have provided supervision, leadership and direction, and intermediate authors have contributed consistent with the CRedIT criteria. When multiple people have made substantial contributions of key experiments and ideas to a project, and where publishing these contributions as a single study is likely to lead to a more impactful paper, then the major contributors will share joing or equal contributing first author status. If at any stage of a project you would like to discuss authorship issues then please mention this to Matt or Gülşen. We aim that all authorship decisions are made collaboratively and with the agreement of all authors. In the even of unresolvable differences then Matt or Gülşen will have responsibility for the final decision.

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SPAD-baseed high speed imaging

Recent progress towards understanding the biological basis for cognition and its disorders has been driven by advances in molecular tools for labelling and manipulation of defined populations of neurons. However, brain circuits operate at a millisecond time scales and our ability to resolve this activity is limited. Electrophysiological methods have the required temporal precision, but do not reliably identify multiple individual neurons within large populations, a pre-requisite for many important questions. In contrast, imaging approaches based on detection of intracellular Ca2+ signals can track activity in large populations of neurons but give only an indirect readout of neuronal activity with limited temporal resolution. New genetically encoded voltage indicators (GEVIs) address many of the shortcomings of Ca2+ imaging. Crucially, they report both action potentials and subthreshold electrical activity in defined neurons with millisecond resolution. However, application of GEVIs will require a new generation of cameras with frame rates sufficient to monitor millisecond scale changes.

We propose to validate cameras based on Single Photon Avalance Diode (SPAD) sensor technology developed in the School of Engineering by Robert Henderson and colleagues. SPADs are electronic devices that when activated by a single photon cause an avalanche of electrons and a large electric current. Because SPADs detect the time at which individual photons arrive, they are well suited to extremely high speed and low light imaging. In contrast, standard camera sensors must bin photons across a time window, which limits their sensitivity and temporal resolution. In our prototype SPAD-based cameras, the sensor chip is a similar size to sensors used in miniature microscopes we currently use for Ca2+ imaging in behaving rodents. It is therefore physically feasible to use SPADs to image activity even in freely behaving animals.

What are the obstacles to application of SPAD technology and how can we overcome them? The key immediate challenge addressed here is to obtain proof-of-principle data that SPAD-based cameras can detect neuronal activity reported with GEVIs. This requires that we introduce viruses encoding GEVIs into a mouse brain, generate known activity patterns in neurons expressing the GEVIs and use the SPAD cameras to image the signal from the GEVIs. With these data, we will be in a strong position to obtain larger funding to develop and validate SPAD-based cameras suitable for widespread use (see Exit Strategy).

References

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research

We aim to understand the cellular and molecular basis for computations that underlie episodic memory.

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research

We aim to understand the cellular and molecular basis for computations that underlie episodic memory.

\ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml index a369e1132e99..bfdb0aa2136f 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1 +1 @@ - https://mattnolanlab.github.io/news/announcement_1/ 2024-03-14T19:35:00+00:00 https://mattnolanlab.github.io/news/HarryPaper/ 2024-03-28T22:42:00+00:00 https://mattnolanlab.github.io/blog/2015/formatting-and-links/ 2015-03-15T16:40:16+00:00 https://mattnolanlab.github.io/blog/2015/images/ 2015-05-15T21:01:00+00:00 https://mattnolanlab.github.io/blog/2015/code/ 2015-07-15T15:09:00+00:00 https://mattnolanlab.github.io/blog/2015/math/ 2015-10-20T15:12:00+00:00 https://mattnolanlab.github.io/blog/2015/disqus-comments/ 2015-10-20T15:59:00+00:00 https://mattnolanlab.github.io/blog/2020/twitter/ 2020-09-28T15:12:00+00:00 https://mattnolanlab.github.io/blog/2020/github-metadata/ 2020-09-28T21:01:00+00:00 https://mattnolanlab.github.io/blog/2021/distill/ 2021-05-22T00:00:00+00:00 https://mattnolanlab.github.io/blog/2021/diagrams/ 2021-07-04T17:39:00+00:00 https://mattnolanlab.github.io/blog/2022/redirect/ 2022-02-01T17:39:00+00:00 https://mattnolanlab.github.io/blog/2022/giscus-comments/ 2022-12-10T15:59:00+00:00 https://mattnolanlab.github.io/blog/2023/table-of-contents/ 2023-03-20T15:59:00+00:00 https://mattnolanlab.github.io/blog/2023/tables/ 2023-03-20T18:37:00+00:00 https://mattnolanlab.github.io/blog/2023/videos/ 2023-04-24T21:01:00+00:00 https://mattnolanlab.github.io/blog/2023/audios/ 2023-04-25T10:25:00+00:00 https://mattnolanlab.github.io/blog/2023/sidebar-table-of-contents/ 2023-04-25T14:14:00+00:00 https://mattnolanlab.github.io/blog/2023/custom-blockquotes/ 2023-05-12T19:53:00+00:00 https://mattnolanlab.github.io/blog/2023/jupyter-notebook/ 2023-07-04T12:57:00+00:00 https://mattnolanlab.github.io/blog/2023/post-bibliography/ 2023-07-12T13:56:00+00:00 https://mattnolanlab.github.io/blog/2023/tikzjax/ 2023-12-12T22:25:00+00:00 https://mattnolanlab.github.io/blog/2024/chartjs/ 2024-01-26T01:04:00+00:00 https://mattnolanlab.github.io/blog/2024/echarts/ 2024-01-26T16:03:00+00:00 https://mattnolanlab.github.io/blog/2024/geojson-map/ 2024-01-26T17:57:00+00:00 https://mattnolanlab.github.io/blog/2024/vega-lite/ 2024-01-27T00:20:00+00:00 https://mattnolanlab.github.io/blog/2024/advanced-images/ 2024-01-27T11:46:00+00:00 https://mattnolanlab.github.io/blog/2024/code-diff/ 2024-01-27T19:22:00+00:00 https://mattnolanlab.github.io/blog/2022/displaying-external-posts-on-your-al-folio-blog/ 2022-04-23T23:20:09+00:00 https://mattnolanlab.github.io/projects/spatial_memory/ 2024-04-10T16:22:05+00:00 https://mattnolanlab.github.io/ https://mattnolanlab.github.io/data-and-code/ https://mattnolanlab.github.io/lab-values/ https://mattnolanlab.github.io/news/ https://mattnolanlab.github.io/nolan-lab/ https://mattnolanlab.github.io/surmeli-lab/ https://mattnolanlab.github.io/publications/ https://mattnolanlab.github.io/research/ 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https://mattnolanlab.github.io/blog/category/external-services/ https://mattnolanlab.github.io/blog/2015/ https://mattnolanlab.github.io/blog/2020/ https://mattnolanlab.github.io/blog/2021/ https://mattnolanlab.github.io/blog/2022/ https://mattnolanlab.github.io/blog/2023/ https://mattnolanlab.github.io/blog/2024/ https://mattnolanlab.github.io/lighthouse_results/desktop/alshedivat_github_io_al_folio_.html 2024-04-10T16:21:39+00:00 https://mattnolanlab.github.io/lighthouse_results/mobile/alshedivat_github_io_al_folio_.html 2024-04-10T16:21:39+00:00 \ No newline at end of file + https://mattnolanlab.github.io/news/announcement_1/ 2024-03-14T19:35:00+00:00 https://mattnolanlab.github.io/news/HarryPaper/ 2024-03-28T22:42:00+00:00 https://mattnolanlab.github.io/blog/2015/formatting-and-links/ 2015-03-15T16:40:16+00:00 https://mattnolanlab.github.io/blog/2015/images/ 2015-05-15T21:01:00+00:00 https://mattnolanlab.github.io/blog/2015/code/ 2015-07-15T15:09:00+00:00 https://mattnolanlab.github.io/blog/2015/math/ 2015-10-20T15:12:00+00:00 https://mattnolanlab.github.io/blog/2015/disqus-comments/ 2015-10-20T15:59:00+00:00 https://mattnolanlab.github.io/blog/2020/twitter/ 2020-09-28T15:12:00+00:00 https://mattnolanlab.github.io/blog/2020/github-metadata/ 2020-09-28T21:01:00+00:00 https://mattnolanlab.github.io/blog/2021/distill/ 2021-05-22T00:00:00+00:00 https://mattnolanlab.github.io/blog/2021/diagrams/ 2021-07-04T17:39:00+00:00 https://mattnolanlab.github.io/blog/2022/redirect/ 2022-02-01T17:39:00+00:00 https://mattnolanlab.github.io/blog/2022/giscus-comments/ 2022-12-10T15:59:00+00:00 https://mattnolanlab.github.io/blog/2023/table-of-contents/ 2023-03-20T15:59:00+00:00 https://mattnolanlab.github.io/blog/2023/tables/ 2023-03-20T18:37:00+00:00 https://mattnolanlab.github.io/blog/2023/videos/ 2023-04-24T21:01:00+00:00 https://mattnolanlab.github.io/blog/2023/audios/ 2023-04-25T10:25:00+00:00 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2022-04-23T23:20:09+00:00 https://mattnolanlab.github.io/projects/high_speed_imaging/ 2024-04-10T16:37:24+00:00 https://mattnolanlab.github.io/projects/spatial_memory/ 2024-04-10T16:37:24+00:00 https://mattnolanlab.github.io/ https://mattnolanlab.github.io/data-and-code/ https://mattnolanlab.github.io/lab-values/ https://mattnolanlab.github.io/news/ https://mattnolanlab.github.io/nolan-lab/ https://mattnolanlab.github.io/surmeli-lab/ https://mattnolanlab.github.io/publications/ https://mattnolanlab.github.io/research/ https://mattnolanlab.github.io/blog/tag/formatting/ https://mattnolanlab.github.io/blog/tag/links/ https://mattnolanlab.github.io/blog/tag/images/ https://mattnolanlab.github.io/blog/tag/code/ https://mattnolanlab.github.io/blog/tag/math/ https://mattnolanlab.github.io/blog/tag/comments/ https://mattnolanlab.github.io/blog/tag/metadata/ https://mattnolanlab.github.io/blog/tag/distill/ https://mattnolanlab.github.io/blog/tag/diagrams/ 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