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8 changes: 7 additions & 1 deletion _sources/courses/multiphoton-analysis.md.txt
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# Multiphoton imaging analysis

## Overview
TBC
This course will be delivered by [Petr Znamenskiy](https://www.crick.ac.uk/research/labs/petr-znamenskiy) and will cover:

* What do the data values in a microscopy image represent? How do they relate to the number of photons hitting the detector?
* Motion correction for 2p imaging
* Segmentation and activity extraction
* Neuropil contamination and what to do about it
* [CaImAn](https://caiman.readthedocs.io/en/latest/) and other end-to-end pipelines

## Prerequisites
TBC
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62 changes: 14 additions & 48 deletions _sources/index.md.txt
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Expand Up @@ -7,25 +7,8 @@ Computational skills training at the [UCL](https://www.ucl.ac.uk/)
::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} {fas}`bolt;sd-text-primary` November 8th & 9th 2023
:link: courses/extracellular-analysis
:link-type: doc

Extracellular electrophysiology analysis
+++
Sainsbury Wellcome Centre, UCL <br>


Wed 8th:
* 9.30am - 12pm (Gatsby Seminar Room)
* 1.30pm - 3.30pm (Gatsby Seminar Room)

Thu 9th:
* 9:00am - 10:45am (Ground Floor Lecture Theatre)
* 12:30pm - 2.00pm (Brasserie Seminar Room)
* 3.30pm - 5.30 pm (Brasserie Seminar Room)
:::

:::{grid-item-card} {fas}`video;sd-text-primary` November 29th 2023
:link: courses/video-analysis
:link-type: doc
Expand All @@ -50,25 +33,19 @@ Ground Floor Lecture Theatre
1pm - 5pm
:::

[//]: # (:::{grid-item-card} {fas}`file-image;sd-text-primary` December 5th 2023)

[//]: # (:link: courses/multiphoton-analysis)

[//]: # (:link-type: doc)

[//]: # ()
[//]: # (Multiphoton imaging analysis)

[//]: # (+++)
:::{grid-item-card} {fas}`file-image;sd-text-primary` December 5th 2023
:link: courses/multiphoton-analysis
:link-type: doc

[//]: # (Sainsbury Wellcome Centre, UCL <br>)
Multiphoton imaging analysis

[//]: # (Room TBC)
+++
Sainsbury Wellcome Centre, UCL <br>
Ground Floor Lecture Theatre

[//]: # ()
[//]: # (2pm - 5pm)
2pm - 5pm

[//]: # (:::)
:::

:::{grid-item-card} {fas}`file-image;sd-text-primary` December 6th 2023
:link: courses/histology-brainglobe
Expand All @@ -90,65 +67,54 @@ Gatsby Seminar Room (3rd floor)
::::{grid} 1 2 2 3
:gutter: 3

:::{grid-item-card} {fas}`bolt;sd-text-primary` Extracellular electrophysiology analysis
:link: courses/extracellular-analysis
:link-type: doc
:::

:::{grid-item-card} {fas}`code;sd-text-primary` Collaborative coding and software development good practices
:link: courses/collaborative-coding
:link-type: doc

:::

:::{grid-item-card} {fas}`floppy-disk;sd-text-primary` Data management and sharing
:link: courses/data-management
:link-type: doc

:::

:::{grid-item-card} {fa}`file-image;sd-text-primary` Image Analysis in Python
:link: courses/image-analysis-python
:link-type: doc


:::

:::{grid-item-card} {fa}`file-image;sd-text-primary` Introduction to Image Analysis
:link: courses/introduction-image-analysis
:link-type: doc


:::

:::{grid-item-card} {fas}`server;sd-text-primary` Introduction to high-performance computing with Linux
:link: courses/HPC-linux
:link-type: doc


:::

:::{grid-item-card} {fas}`wave-square;sd-text-primary` Introduction to Timeseries Analysis in Python
:link: courses/timeseries-analysis
:link-type: doc


:::

:::{grid-item-card} {fas}`code;sd-text-primary` Turning your Python scripts into reusable, general-purpose software
:link: courses/python-packaging
:link-type: doc


:::

:::{grid-item-card} {fas}`code;sd-text-primary` Type annotation in Python
:link: courses/type-annotation
:link-type: doc


:::

:::{grid-item-card} {fas}`code;sd-text-primary` Introduction to Software Development in Python
:link: courses/intro-software-dev
:link-type: doc


:::

::::
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9 changes: 8 additions & 1 deletion courses/multiphoton-analysis.html
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Expand Up @@ -369,7 +369,14 @@
<h1>Multiphoton imaging analysis<a class="headerlink" href="#multiphoton-imaging-analysis" title="Link to this heading">#</a></h1>
<section id="overview">
<h2>Overview<a class="headerlink" href="#overview" title="Link to this heading">#</a></h2>
<p>TBC</p>
<p>This course will be delivered by <a class="reference external" href="https://www.crick.ac.uk/research/labs/petr-znamenskiy">Petr Znamenskiy</a> and will cover:</p>
<ul class="simple">
<li><p>What do the data values in a microscopy image represent? How do they relate to the number of photons hitting the detector?</p></li>
<li><p>Motion correction for 2p imaging</p></li>
<li><p>Segmentation and activity extraction</p></li>
<li><p>Neuropil contamination and what to do about it</p></li>
<li><p><a class="reference external" href="https://caiman.readthedocs.io/en/latest/">CaImAn</a> and other end-to-end pipelines</p></li>
</ul>
</section>
<section id="prerequisites">
<h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Link to this heading">#</a></h2>
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45 changes: 22 additions & 23 deletions index.html
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Expand Up @@ -322,29 +322,6 @@ <h2>Upcoming Courses<a class="headerlink" href="#upcoming-courses" title="Link t
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-bolt sd-text-primary"></span> November 8th &amp; 9th 2023</div>
<p class="sd-card-text">Extracellular electrophysiology analysis</p>
</div>
<div class="sd-card-footer docutils">
<p class="sd-card-text">Sainsbury Wellcome Centre, UCL <br></p>
<p class="sd-card-text">Wed 8th:</p>
<ul class="simple">
<li><p class="sd-card-text">9.30am - 12pm (Gatsby Seminar Room)</p></li>
<li><p class="sd-card-text">1.30pm - 3.30pm (Gatsby Seminar Room)</p></li>
</ul>
<p class="sd-card-text">Thu 9th:</p>
<ul class="simple">
<li><p class="sd-card-text">9:00am - 10:45am (Ground Floor Lecture Theatre)</p></li>
<li><p class="sd-card-text">12:30pm - 2.00pm (Brasserie Seminar Room)</p></li>
<li><p class="sd-card-text">3.30pm - 5.30 pm (Brasserie Seminar Room)</p></li>
</ul>
</div>
<a class="sd-stretched-link reference internal" href="courses/extracellular-analysis.html"><span class="doc"></span></a></div>
</div>
<div class="sd-col sd-d-flex-row docutils">
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-video sd-text-primary"></span> November 29th 2023</div>
<p class="sd-card-text">Video-based analysis of animal behaviour</p>
</div>
Expand Down Expand Up @@ -373,6 +350,20 @@ <h2>Upcoming Courses<a class="headerlink" href="#upcoming-courses" title="Link t
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-file-image sd-text-primary"></span> December 5th 2023</div>
<p class="sd-card-text">Multiphoton imaging analysis</p>
</div>
<div class="sd-card-footer docutils">
<p class="sd-card-text">Sainsbury Wellcome Centre, UCL <br>
Ground Floor Lecture Theatre</p>
<p class="sd-card-text">2pm - 5pm</p>
</div>
<a class="sd-stretched-link reference internal" href="courses/multiphoton-analysis.html"><span class="doc"></span></a></div>
</div>
<div class="sd-col sd-d-flex-row docutils">
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-file-image sd-text-primary"></span> December 6th 2023</div>
<p class="sd-card-text">Histology analysis using napari and BrainGlobe</p>
</div>
Expand All @@ -395,6 +386,14 @@ <h2>Previous Courses<a class="headerlink" href="#previous-courses" title="Link t
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-bolt sd-text-primary"></span> Extracellular electrophysiology analysis</div>
</div>
<a class="sd-stretched-link reference internal" href="courses/extracellular-analysis.html"><span class="doc"></span></a></div>
</div>
<div class="sd-col sd-d-flex-row docutils">
<div class="sd-card sd-sphinx-override sd-w-100 sd-shadow-sm sd-card-hover docutils">
<div class="sd-card-body docutils">
<div class="sd-card-title sd-font-weight-bold docutils">
<span class="fas fa-code sd-text-primary"></span> Collaborative coding and software development good practices</div>
</div>
<a class="sd-stretched-link reference internal" href="courses/collaborative-coding.html"><span class="doc"></span></a></div>
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