| Name | CalSciPy JSON |
| Version |
0.8.3
JSON |
| download |
| home_page | None |
| Summary | A toolbox for analyzing, designing, and visualizing multiphoton imaging & optogenetics experiments. |
| upload_time | 2024-03-27 17:45:37 |
| maintainer | Darik A. O'Neil |
| docs_url | None |
| author | Darik A. O'Neil |
| requires_python | <4,>=3.8 |
| license | MIT License Copyright (c) 2023 Darik A O’Neil Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
calscipy
calcium imaging
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## CalSciPy
<!-- Line 1 Badges... PyPi, Downloads, Maintained, Coverage, Documentation -->
<!-- Line 2 Badges... Python Versions, PyPi Status, License, Contributors -->
[](https://coveralls.io/github/darikoneil/CalSciPy?branch=master)
[](https://calscipy.readthedocs.io/en/latest/?badge=latest)
CalSciPy is a utility toolbox for calcium imaging experiments. It contains a variety of useful features, from
interactive visualization of data to computer-generated holography for "read/write" experiments, and
everything in-between. Essentially, it's a collection of code written for my imaging experiments that might be
considered useful to others. I was inspired to upload my own code to solve some of the issues outlined in the [motivation](https://calscipy.readthedocs.io/en/latest/introduction__motivation.html) section of the [docs](https://calscipy.readthedocs.io/en/latest/index.html#) or at least create a neat package my friends and I could use to easily analyze data across various environments and computers.
#### Active Development
As of version 0.9.8, the current implementation is unstable, partially untested, partially finished, and should be considered an open alpha/beta. ***Please be patient, refactoring my code for public use is a pet-project. I have to graduate at some point and I have a newborn.***
Until things are more stable, I'll explicitly note which subpackages are stable, have >90% test coverage, and are ready-to-use.
#### Stable & Tested Modules
* The main module is ready to use as of 0.7.5. New features will be demarcated by a label indicating the version added in the docs.
#### Experimental
* The organization module is untested but incorporated into the distributed pypi version
* The bruker module is untested but incorporated into the distributed pypi version
* The optogenetics module is untested but incorporated into the distributed pypi version
#### Unstable
* The interactive module is unstable but partially incorporated into the distributed pypi version
* The optics module is unstable and not incorporated into the distributed pypi version
#### Installation
Eventually I will break things up into sub-packages so you don't have to install everything together...
`pip install CalSciPy`
#### Roadmap
My current focus is on refactoring tools for holographic optogenetics and circumventing PrairieView's writing of data to proprietary RAW format. I also plan on
breaking up this repo because its many of its contents are too decoupled (e.g., bruker prairieview tricks / helpers vs experiment organization)
#### Contributions
Save me from myself, contributions welcome :)
#### Documentation
Hosted at [ReadtheDocs](https://calscipy.readthedocs.io/en/latest/index.html#).
Available locally as [HTML](https://github.com/darikoneil/CalSciPy/tree/master/docs/build/html), [LATEX](https://github.com/darikoneil/CalSciPy/tree/master/docs/build/latex) and [PDF](https://github.com/darikoneil/CalSciPy/blob/master/docs/build/pdf/calscipy.pdf).
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"license": "MIT License Copyright (c) 2023 Darik A O\u2019Neil Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the \"Software\"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ",
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