zapit

General purpose optostimulation system

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Updated Thu, 17 Aug 2023 14:12:41 +0000

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Zapit

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Zapit is software that runs a scanning opto-stim system for head-fixed mouse behavior.

How it works

A pair of scan mirrors deflect an incoming laser beam, which is focused onto the exposed skull with a lens. This lens is also used to image the sample onto a camera in order to visualise where the beam is pointing. Zapit registers the scanners to the camera, allowing the user to place the beam in any desired location by clicking there on a live image feed. Zapit then registers stereotaxic coordinates into the camera space, allowing the user to point the beam to coordinates defined with respect to bregma. A graphical tool builds experiment coordinate files using a top-down view of the Allen Atlas. There is a simple MATLAB API for integrating stimulation into existing behavioral code and a Python version of the API is also provided.

Install & Usage

See the Installation & User Manual. Please see the list of known obvious bugs and issues. There is a Change Log if you are concerned about applying updates.

Requirements

If any of the above Toolboxes are included in your licence but not installed, you may install them using the Add On Manager.

Contributing

Code was written by Maja Skretowska and Rob Campbell at the Sainsbury Wellcome Centre (UCL) in 2021/2022. Contributions and collaborations are welcome. Please see the CONTRIBUTING.md file for more information.

Related Projects

Inspiration

This project was inspired by studies from Svoboda and Tank and Brody.

Cite As

Rob Campbell (2023). zapit (https://github.com/Zapit-Optostim/zapit/releases/tag/v0.12.1), GitHub. Retrieved .

MATLAB Release Compatibility
Created with R2022b
Compatible with any release
Platform Compatibility
Windows macOS Linux

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development

development/@testCamera

development/mainGUI

development/recordWaveforms

development/stimConfigGUI

development/stimuli

examples/externalTrigger

examples/minimalWaveformPresentation

examples/running_experiments

tests

tests/interactive

zapit

zapit/+zapit

zapit/+zapit/+gui/+main

zapit/+zapit/+gui/+main/@controller

zapit/+zapit/+gui/+stimConfigEditor

zapit/+zapit/+gui/+stimConfigEditor/@controller

zapit/+zapit/+hardware

zapit/+zapit/+hardware/+DAQ/@dotNETwrapper

zapit/+zapit/+hardware/+DAQ/@vidriowrapper

zapit/+zapit/+hardware/+vidrio_daqmx

zapit/+zapit/+hardware/+vidrio_daqmx/+idioms

zapit/+zapit/+hardware/+vidrio_daqmx/+private

zapit/+zapit/+hardware/+vidrio_daqmx/+util

zapit/+zapit/+hardware/+vidrio_daqmx/@Task

zapit/+zapit/+hardware/+vidrio_daqmx/private

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_19_0_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_19_1_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_19_5_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_19_6_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_20_0_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_20_1_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_20_7_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_21_0_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_21_3_x/x64

zapit/+zapit/+hardware/+vidrio_daqmx/private/NIDAQmx_21_8_x/x64

zapit/+zapit/+hardware/@camera

zapit/+zapit/+interfaces

zapit/+zapit/+interfaces/@TCPserver

zapit/+zapit/+settings

zapit/+zapit/+simulated/@DAQ

zapit/+zapit/+simulated/@camera

zapit/+zapit/+stimConfig

zapit/+zapit/+updater

zapit/+zapit/+utils

zapit/+zapit/+yaml

zapit/+zapit/+yaml/Tests

zapit/+zapit/+yaml/extras

zapit/+zapit/@pointer

zapit/+zapit/@stimConfig

Version Published Release Notes
0.12.1.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.12.1

0.12.0.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.12.0

0.11.1.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.11.1

0.11.0.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.11.0

0.10.6.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.6

0.10.5.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.5

0.10.4.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.4

0.10.3.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.3

0.10.2.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.2

0.10.0

See release notes for this release on GitHub: https://github.com/Zapit-Optostim/zapit/releases/tag/v0.10.0

0.1.1

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.