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neuroscience imaging analysis tools: 2023 update
14 september 2023 | neuroscience
An updated resource that provides new and existing researchers a central location for methods and URLs for (calcium) imaging data processin[...]g 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.

long-term optical imaging of the spinal cord in awake, behaving animals
25 may 2023 | neuroscience
How does the spinal cord process sensory stimuli in awake animals? A brief overview of results from our recent preprint describing [...]a spinal implant chamber, fibrosis-inhibiting materials, computational methods, and end-to-end pipeline for large-scale bilateral recording from multiple segments of the spinal cord. This allowed us to conduct long-term (months to over a year) imaging of individual axons, microglia dynamics, and Ca2+ imaging of neurons—all in awake, behaving animals.

Several of the approaches described, such as fibrosis inhibition, are applicable to preparations and experiments beyond the spinal cord.

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!

neuroscience imaging analysis tools
08 november 2021 | neuroscience
Provide 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.

The table can be sorted by column by clicking each header.

Also found as part of the Brain Initiative Notes post imaging analysis tools or https://github.com/bahanonu/imaging_tools.

spatiotemporal domain of neuroscience methods
29 may 2019 | neuroscience
An updated spatiotemporal domain of neuroscience methods graphic, inspired by from Sejnow[...]ski, 2014. More changes will be added in time.

the return of the brain initiative notes
09 december 2018 | neuroscience
I will begin posting again on the BRAIN initiative notes running webpage/blog that I started while ago. There is a lot going on in neurosci[...]ence and many questions of how it relates to society at large. Below I have included the first of the new posts that goes over methods for identifying cells and reconstructing neural activity traces from calcium imaging movies.

Find article on BRAIN webpage at Calcium imaging cell identification and fluorescence activity trace reconstruction, part 1.

Look forward to more postings!

neuroscience and biology technologies
30 november 2014 | neuroscience
Earlier this year I created a webpage to list various labs, websites, and other resources related to neuroscience and biotechnology. Decide[...]d to expand on this and create a living document of various technologies currently used in neuroscience.

brain initiative notes
27 may 2013 | neuroscience
This is a continually updated collection of news, ideas/findings, and other tidbits related to the [...]n/' target='_blank'>BRAIN initiative, promising biotechnologies, and neuroscience/biology in general. This is a really exciting time in neuroscience and I hope to capture a bit of that here.

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