Merge branch 'master' of github.com:MattNolanLab/MattNolanLab.github.io

_pages/values.md

@@ -6,80 +6,37 @@ nav: true
 nav_order: 7
 ---
 
-This document is inspired by Mariam Aly’s excellent [article](https://www.nature.com/articles/d41586-018-06167-w) about lab manuals and by her lab’s [manual](https://www.alylab.org/). This page contains information about the lab [goals](#goals), [expectations and responsibilities](#er) and [publication policies](#pub). Information about mailing lists, calendars, contact numbers, computing resources, animal management and experimental protocols is on our internal [wiki](https://www.wiki.ed.ac.uk/pages/viewpage.action?pageId=376674941).
+This document is inspired by Mariam Aly’s excellent [article](https://www.nature.com/articles/d41586-018-06167-w). This page contains brief information about the lab [goals](#goals), [expectations and responsibilities](#er) and [publication policies](#pub). 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](https://www.wiki.ed.ac.uk/pages/viewpage.action?pageId=376674941).
 
 ### Goals {#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. We expect everyone in our labs to share this commitment. We also do our best to make the process fun.
+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 {#er}
-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. 
+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](https://www.wiki.ed.ac.uk/pages/viewpage.action?pageId=376674941). 
 
-#### Everyone
+##### *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.
--  Act respectfully at all times towards fellow lab members, colleagues and the public at large. This includes following the University's dignitiy and respect policy.
-- Ask questions. Everyone has a right to ask questions and seniority is no guarantee of having the right answer.
-- Base arguments and decisions on sound theory and evidence.
-- Maintaining a healthy work life balance is important for you and your colleagues.
-- Recognise and give credit to other people for their ideas and contributions. This includes your lab colleagues and people outside the lab.
-- Be aware of the broader context in which we work. This includes the relevance of what we do for the wider public and effects on the environment of travel and general use of resources.
 
-As well as good ideas good science requires experiments that are rigorous and reproducible.
-- Experiments are often difficult and can take time to get working well. It’s as important to share problems as successes. We can all learn from problems and other people may have helpful suggestions.
-- Design your experiments carefully to address a clear question. When relevant ensure appropriate consideration of statistical design issues including power, effect size, group size and blinding.
-- Ensure your data is of the best quality you can achieve. Have clear pre-defined criteria for data quality and don’t spend time on data that don’t reach these criteria. If you’re developing a new method then develop quality criteria.
-- Ensure that your research is reproducible. This includes documenting methods and where possible implementing analyses in code so they can be repeated using raw data as an input.
+##### *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.
 
-#### 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. Ways we try to achieve these goals include:
-- Setting big picture scientific goals and objectives.
-- Helping you to develop your research and provide opportunities for training.
-- Meeting regularly with you and being available for ad hoc meetings.
-- Giving feedback and perspectives on projects and the field more generally.
-- Obtaining resources for lab projects.
-- Supporting your applications for funding.
-- Providing advice and support for future stages of your career.
-- Working with you to write up projects for publication.
+##### *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.
 
-#### Postdocs, research staff and PhD students
-We expect postdocs and PhD students to lead research project addressing questions within the big picture goals of the Sürmeli and Nolan labs. 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.
-
-To achive these goals we expect you to:
-- Work with Gülşen and / or Matt to set your research goals and prioritise your commitments.
-- Arrange training to meet your project goals. Gülşen or Matt will help you identify other lab members or collaborators to contribute to your training.
-- Maintain careful records of lab methods, including training received, and of all experiments.
-- Work independently towards your project goals. We expect you to encounter challenges and obstacles. We suggest problem solving in the following order: 1, review your notes and records to identifiy overlooked issues; 2, consult the wiki, equipment manuals and / or published protocols; 3, consult with lab colleagues (we put this third as this way you save your colleagues time for the most important problems, while following steps 1 and 2 will also more effectively develop your expertise); 4, discuss with Gülşen or Matt. If your trouble shooting identifies alternative strategies, this is very welcome, but be sure to discuss with Gülşen or Matt and your collaborators before initiating major changes of direction.
-- Share your expertise with other group members.
-- Identify skills and expertise you would like to develop and take advantage of opportunities to do so. We expect everyone to use at least 10 days per year for training or other professional development.
-- Keep up to date with detailed literature in your field and important advances across neurocience in general.
-- Contribute to supervision of MSc and undergraduate research students.
-- Take holidays and aim to maintain a healthy work-like balance.
-
-
-
-#### Masters and undergraduate students
+##### *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
 
-We expect you to take excellent notes on your training and to follow these when carrying out experiments. 
-You very likely will still encounter unexpected challenges. 
-We suggest problem solving in the following order: 
-1. Review your notes and records to check if there are any issues you've overlooked. 
-2. Consult with the person supervising you. You should not change or modify protocols without consulting with the person supervising you; this will very likely end up wasting your time and lab resources.
-
-You will meet regularly with Gülşen and / or Matt to discuss your work and plans.
-
-You should read literature around your project and more generally.
-
 
 
 ### Publication policies {#pub}
 
-#### 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 prefers.
+##### *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
+##### *Data and code*
 We aim to share all data and code, see [data & code](/data-and-code).
 
-#### Authorship
+##### *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.

_projects/high_speed_imaging.md

@@ -0,0 +1,31 @@
+---
+layout: page
+title: High speed imaging
+importance: 1
+category: work
+related_publications: true
+img: assets/img/SPADspikes_zoom.jpeg
+---
+
+We are collaborating with Istvan Gyongy, Srinjoy Mitra and Robert Henderson in the School of Engineering in Edinburgh to develop applications of single photon avalanche diode (SPAD) technology to imaging of neural activity.
+
+#### Rationale
+
+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.
+
+
+#### Goals
+
+We are developing and validating neuroscience applications of SPAD sensor technology developed by our collaborators. 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.
+
+
+#### Progress
+
+We published the first proof-of-principle demonstration that SPAD-based cameras can detect neuronal activity reported with GEVIs (Tian et al. 2022). This required introducing viruses encoding GEVIs into a mouse brain, generate known activity patterns in neurons expressing the GEVIs and using SPAD cameras to image the signal from the GEVIs (see figure).
+
+We are now evaluating new generation SPAD devices and working to miniaturise SPAD cameras for imaging in freely moving animals.
+