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Update README.md
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kushalkolar authored Sep 20, 2022
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Expand Up @@ -23,13 +23,31 @@ We recommend starting out with the demo notebook ```notebooks/mcorr_cnmf.ipynb``
Documentation is available at: https://mesmerize-core.readthedocs.io/ \
User guide: https://mesmerize-core.readthedocs.io/en/latest/user_guide.html

# Overview

![batch_management](https://user-images.githubusercontent.com/9403332/179145962-82317da6-0340-44e4-83ba-7dace0300f55.png)

# Visualization

For visualization we recommend [`mesmerize-viz`](https://github.com/kushalkolar/mesmerize-viz) which contains a standard set of visualizations (a WIP), or [`fastplotlib`](https://github.com/kushalkolar/fastplotlib). You can also use the [`mesmerize-napari`](https://github.com/nel-lab/mesmerize-napari) plugin for small datasets.
For visualization we recommend [`mesmerize-viz`](https://github.com/kushalkolar/mesmerize-viz) which contains a standard set of visualizations (a WIP), or [`fastplotlib`](https://github.com/kushalkolar/fastplotlib). Here are some examples of visualizations using `fastplotlib`, these visualizations are all performed within jupyter notebooks therefore they will also work on cloud computing intrastructure!

# Overview
View raw and motion corrected movie side by side:

![batch_management](https://user-images.githubusercontent.com/9403332/179145962-82317da6-0340-44e4-83ba-7dace0300f55.png)
https://user-images.githubusercontent.com/9403332/191207398-39a027d7-079e-475b-baec-381f2d271652.mp4

Contours from CNMF, good components in cyan and bad components in magenta:

https://user-images.githubusercontent.com/9403332/191207461-9c5c4cad-867b-413a-b30b-ea61f010eed6.mp4

Input movie, constructed movie `(A * C)`, residuals `(Y - A * C - b * f)`, and reconstructed background (b * f):

https://user-images.githubusercontent.com/9403332/191207782-566e24bc-7f0d-40a3-9442-37c86d0ebe48.mp4

Interactive Component evaluation after CNMF:

https://user-images.githubusercontent.com/9403332/191207883-2393664d-b5e1-49a5-84d1-8ed7eadcf7a0.mp4

This is all possible within jupyter notebooks using `fastplotlib`!

# Installation

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