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AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data
https://allensdk.readthedocs.io/en/latest/
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Update AllenSDK docs for Brain Observatory #1984

Closed wbwakeman closed 3 years ago

wbwakeman commented 3 years ago

https://allensdk.readthedocs.io/en/latest/brain_observatory.html https://allensdk.readthedocs.io/en/latest/visual_coding_neuropixels.html

Add documentation for Image Change Detection 2-photon similar to these other pages for Visual Coding 2-p and Visual Coding - Neuropixels

Based on content, text and notebooks provided by Visual Behavior project.

Marina will provide a Word doc with the content, and one or more notebooks.

https://github.com/AllenInstitute/AllenSDK/blob/master/doc_template/brain_observatory_nwb.rst

Tasks:

Validation criteria:

wbwakeman commented 3 years ago

@matchings @dougollerenshaw May I request some content that we can use to fill out this page for the Visual Behavior project? Specifically, we are looking for a Word document that has content for the page, and whatever notebooks should be included

matchings commented 3 years ago

@wbwakeman yes. What is the timeline for this?

wbwakeman commented 3 years ago

@matchings Can we say by EOD Tuesday, March 23?

matchings commented 3 years ago

@wbwakeman yeah that should be no problem.

wbwakeman commented 3 years ago

Sooner is always better :-)

matchings commented 3 years ago

We will probably have it sooner because we need similar content for the white paper and the CMS, which are both needed asap as well

Matyasz commented 3 years ago

@matchings Hi Marina, is there any update on this?

matchings commented 3 years ago

@Matyasz thanks for checking in, content creation is currently in progress. its at the top of my list. Should be done in the next day or so.

Matyasz commented 3 years ago

@matchings Hi Marina, has there been any new progress on this?

matchings commented 3 years ago

@Matyasz yes, i will share a link to a document with this information with you on Slack right now

wbwakeman commented 3 years ago

New text to replace the existing Allen Brain Observatory section of https://github.com/AllenInstitute/AllenSDK/blob/master/doc_template/index.rst The Allen Brain Observatory is a collection of data resources for understanding sensory processing in the mouse visual cortex. These resources systematically measure visual responses in multiple cortical areas and layers using two-photon calcium imaging or high-density extracellular electrophysiology (Neuropixels) probes. Recordings are performed on mice passively viewing visual stimuli or trained to actively perform an image change detection task. Behavior Modality Resource Initial release Passive Optical physiology Visual Coding – Optical Physiology June 2016 Passive Extracellular electrophysiology Visual Coding - Neuropixels October 2019 Active Optical physiology Visual Behavior – Optical Physiology March 2021 Active Extracellular electrophysiology Visual Behavior - Neuropixels Coming soon…

Experiment and stimulus data are provided in Neurodata Without Borders (NWB) files. The AllenSDK provides code to: • download and organize experiment data according to cortical area, imaging depth, and Cre line • access experiment metadata and data streams • transform and analyze data
More information about each study is provided in the linked pages. A web-based entry point to the Visual Coding – Optical physiology data is available at http://observatory.brain-map.org/visualcoding .

(Will send Word doc with formatting to @Matyasz in Slack)