neuroscience imaging analysis tools: 2023 update

Summary

An updated resource that provides new and existing researchers a central location for methods and URLs for (calcium) imaging data processing and analysis tools.

This table also includes imaging data handling and analysis tools beyond calcium imaging and will be updated going forward.

Also found at https://bahanonu.com/brain/imaging_tools/ or https://github.com/bahanonu/imaging_tools.

Calcium imaging analysis with CIAtah (https://github.com/bahanonu/ciatah).
Imaging analysis tools, a table by Biafra Ahanonu, PhD

Imaging analysis tools


Updated: 13 September 2023 | Started: 01 December 2018

-biafra
bahanonu [at] alum.mit.edu

more articles to enjoy:

imaging pain-related neural activity in freely-moving animals
30 may 2022 | neuroscience

Our book chapter detailing the entire pipeline from surgeries to analysis for calcium imaging of pain-related neural activity has been publ[...]ished.

This can prove a useful reference for those new to calcium imaging (esp. in freely moving animals) or researchers who want to see how others perform certain experimental and analytical steps along with the rationale. Please reach out if you have any specific questions, happy to help!

why we need more james polks
25 september 2012 | politics

James J. Polk expanded the territory of the United States by about one-third during his tenure. A remarkable feat. Not only that, but i[...]t was done through an astonishing three ways: territorial conquest, gold and negotiation.

Some thoughts on why we should demand less rhetoric and more pragmatism/details from our presidents.

week 2 | day and night
19 june 2012 | singapore

This pace can't keep up. Saw some crazy animals at a night safari, wandered around NUS's campus late at night (the place is chaotic, beauti[...]ful and slightly eerie at night), met with SUTD's president and more. It seems that staying in Singapore for most of the summer is a go, there is so much here to find out and explore. That might also be because I severely underestimated the size of the country (e.g. don't glance at a map's scale and assume 20 miles = 2 miles, haha). Anyhow, here goes, another eventful week summarized in small snippets.

Stanford biology retreat 2014 tshirt
06 September 2014 | designs

Simple design I had for the Stanford biology 2014 retreat. Focused on a molecular structure of DNA and a pipette, a commonly used device in[...] biology.

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