Here we will curate and annotate a list of useful sites that may help new members of our group and those looking for both education in microscopy, calcium imaging, analysis and other resources.
Atlases
The Allen Brain Institute provides exceptional neurobiological references including Cell Types and expression databases, Connectivity Atlas, Histological at of Brain and Spinal Cord, and many others.
Allen Brain Atlases http://portal.brain-map.org/
Neuronal atlas of the dorsal horn as published in Häring et al. Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types. Nat Neurosci. 2018 Jun;21(6):869-880. doi: 10.1038/s41593-018-0141-1. Epub 2018 Apr 23. PMID: 29686262
https://linnarssonlab.org/dorsalhorn/
Opportunities for formal training
The Allen institute
The Allen Institute offers a wide variety of topic oriented in person training options at conferences or a seminars.
https://alleninstitute.org/events-training/
Cold Spring Harbor
Imaging Structure & Function in the Nervous System
July 23 – August 12, 2019
Application Deadline: April 1, 2019
Methods taught will include multi-photon and light-sheet microscopy, and combination of imaging with optogenetics.
https://meetings.cshl.edu/courses.aspx?course=C-IMAG&year=19
Max Planck Florida Institute
Feb. 18 – Mar. 2, 2019
Deadline: Dec 4, 2018
Applying imaging techniques to neuroscience research
https://www.maxplanckflorida.org/education/short-course
Data Analysis Toolboxes
Toolbox-Romano-et-al
- Runs in Matlab
- Maintained by the Zebrafish Neuroethology lab (http://www.zebrain.biologie.ens.fr/)
- Updated November 2017
https://github.com/zebrain-lab/Toolbox-Romano-et-al
Literature: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005526
CaImAn
- Available for Matlab or python
- Maintained by the Flatiron Institute
- Updated Jan 2016
https://github.com/flatironinstitute/CaImAn
Literature: https://elifesciences.org/articles/28728
https://www.sciencedirect.com/science/article/pii/S0896627315010843?via%3Dihub
FISSA (Fast Image Signal Separation Analysis)
- Runs in python
- Maintained by Rochefort Lab
- Updated Feb 2018
https://github.com/rochefort-lab/fissa
Literature: https://www.nature.com/articles/s41598-018-21640-2
Suite2P
- Runs in Matlab
- Maintained by Cortexlab (Kenneth Harris and Matteo Carandini)
- Updated Feb 2018
https://github.com/cortex-lab/Suite2P
Literature: https://www.biorxiv.org/content/early/2017/07/20/061507
https://elifesciences.org/articles/26839
Allen SDK (for analyzing the data in the brain observatory data)
- Runs in Python
- Maintained by the Allen Institute for Brain Science
- Updated Jan 2017
http://alleninstitute.github.io/AllenSDK/data_resources.html
https://github.com/AllenInstitute/AllenSDK
Literature:
https://elifesciences.org/articles/18372 (supplement)
Upcoming Meetings
Neuroscience 2019
October 19th 2019 to October 23rd 2019
Chicago, Illinois, US
Other useful websites
Labrigger is curated by Spencer L. Smith and is a blog and discussion point for research and imaging. He has numerous useful articles discussing new developments in multiphoton imaging, hardware, software, and ‘how to’ articles.