Update course list

docs/source/conf.py

@@ -116,3 +116,5 @@
     "footer_start": ["footer_start"],
     "footer_end": ["footer_end"]
 }
+
+linkcheck_ignore = ["https://keras.io/", "https://wiki.ucl.ac.uk"]

docs/source/courses/multiphoton-analysis.md

@@ -1,7 +1,13 @@
 # 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

docs/source/index.md

@@ -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
@@ -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
@@ -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
-
-
 :::
 
 ::::