arayabrain · sanglevinh · Dec 23, 2024 · Dec 26, 2024 · Dec 26, 2024 · Dec 26, 2024
diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - run: python -m pip install flake8
       - uses: liskin/gh-problem-matcher-wrap@a89a18291dcde8d4e6158adf736b5432987bbf95
         with:
@@ -26,7 +26,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.9'
       - run: python -m pip install isort
       - uses: liskin/gh-problem-matcher-wrap@a89a18291dcde8d4e6158adf736b5432987bbf95
         with:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 default_language_version:
-    python: python3.8
+    python: python3.9
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# optinist <img src="docs/_static/optinist.png" width="250" title="optinist" alt="optinist" align="right" vspace = "50">
+# OptiNiSt <img src="docs/_static/optinist.png" width="250" title="optinist" alt="optinist" align="right" vspace = "50">
 
 <p align="center">
     <a>
@@ -33,23 +33,20 @@ OptiNiSt helps researchers try multiple data analysis methods, visualize the res
 
 OptiNiSt also supports reproducibility of scientific research, standardization of analysis protocols, and developments of novel analysis tools as plug-in.
 
-## Support library
-
-### ROI detection
+### Support Library
 
+#### ROI detection
 - [x] [Suite2p](https://github.com/MouseLand/suite2p)
 - [x] [CaImAn](https://github.com/flatironinstitute/CaImAn)
 - [x] [LCCD](https://github.com/magnetizedCell/lccd-python)
 
-### Postprocessing
-
-- [x] Basic Neural Analysis(Event Trigger Average...)
-- [x] Dimension Reduction(PCA...)
-- [x] Neural Decoding(LDA...)
-- [x] Neural Population Analysis(Correlation...)
-
-### Saving Format
+#### Postprocessing
+- [x] Basic Neural Analysis (Event Trigger Average...)
+- [x] Dimension Reduction (PCA...)
+- [x] Neural Decoding (LDA...)
+- [x] Neural Population Analysis (Correlation...)
 
+#### Saving Format
 - [x] [NWB](https://github.com/NeurodataWithoutBorders/pynwb)
 
 ## Key Features
@@ -71,7 +68,7 @@ OptiNiSt also supports reproducibility of scientific research, standardization o
 Need anaconda or miniconda or miniforge environment.
 
 ```
-conda create -n optinist python=3.8
+conda create -n optinist python=3.9
 conda activate optinist
 ```
 
@@ -137,15 +134,29 @@ Kenji Doya, Yukako Yamane [OIST Neural Computation Unit](https://groups.oist.jp/
 [[LCCD]](https://github.com/magnetizedCell/lccd-python) Tsubasa Ito, Keisuke Ota, Kanako Ueno, Yasuhiro Oisi, Chie Matsubara, Kenta Kobayashi, Masamichi Ohkura, Junichi Nakai, Masanori Murayama, Toru Aonishi, "Low computational-cost cell detection method for calcium imaging data", 2022
 [[PyNWB]](https://github.com/NeurodataWithoutBorders/pynwb) Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Ivan Soltesz, Karel Svoboda, Loren Frank, Kristofer E. Bouchard, "The Neurodata Without Borders ecosystem for neurophysiological data science", bioRxiv 2021.03.13.435173, March 15, 2021
 
-<!-- ## Citing the Project
-To cite this repository in publications:
+
+
+## Citation
+<table width="100%">
+<tr>
+<td valign="top" width="50%">
+If you use this software, please cite our paper:
+<a href="https://www.biorxiv.org/content/10.1101/2024.09.17.613603v1">https://www.biorxiv.org/content/10.1101/2024.09.17.613603v1</a>
+</td>
+<td valign="top" width="50%" align="right">
+<img src="docs/_static/paper_QR.png" alt="Read our paper" width="150">
+</td>
+</tr>
+</table>
+
 ```
 @misc{OptiNiSt,
-  author = {name},
-  title = {title},
-  year = {2022},
-  publisher = {},
-  journal = {},
-  howpublished = {},
+	author = {Yamane, Yukako and Li, Yuzhe and Matsumoto, Keita and Kanai, Ryota and Desforges, Miles and Gutierrez, Carlos Enrique and Doya, Kenji},
+	title = {Optical Neuroimage Studio (OptiNiSt): intuitive, scalable, extendable framework for optical neuroimage data analysis},
+	elocation-id = {2024.09.17.613603},
+	year = {2024},
+	doi = {10.1101/2024.09.17.613603},
+  journal = {bioRxiv}
+	publisher = {Cold Spring Harbor Laboratory},
 }
-``` -->
+```
diff --git a/docs/_static/paper_QR.png b/docs/_static/paper_QR.png
diff --git a/docs/installation/developers/native_platforms_developer.md b/docs/installation/developers/native_platforms_developer.md
@@ -24,7 +24,7 @@ Follow the steps in the `Install Tools` section for each platform below.
   - Mac
     - [Install Tools](../users/mac.md#install-tools)
   - Windows WSL
-    - [Install Tools](../users/windows_native.md#install-tools)
+    - [Install Tools](../users/windows_wsl.md#install-tools)
 - Other platforms
   - Windows Native
     - [Install Tools](../users/windows_native.md#install-tools)
@@ -45,7 +45,7 @@ npm install -g yarn
 ### Create Conda Environment
 
 ```bash
-conda create -n optinist_dev python=3.8 poetry
+conda create -n optinist_dev python=3.9 poetry
 conda activate optinist_dev
 ```
 

diff --git a/docs/installation/users/linux.md b/docs/installation/users/linux.md
@@ -46,7 +46,7 @@ conda config --set channel_priority flexible
 ### Create Conda Environment
 
 ```bash
-conda create -n optinist python=3.8
+conda create -n optinist python=3.9
 conda activate optinist
 ```
 

diff --git a/docs/installation/users/mac.md b/docs/installation/users/mac.md
@@ -60,7 +60,7 @@ conda config --set channel_priority flexible
 ### Create Conda Environment
 
 ```bash
-conda create -n optinist python=3.8
+conda create -n optinist python=3.9
 conda activate optinist
 ```
 

diff --git a/docs/installation/users/windows_native.md b/docs/installation/users/windows_native.md
@@ -48,7 +48,7 @@ On the Terminal (Miniforge Prompt, etc)
 On the Terminal
 
 ```bash
-conda create -n optinist python=3.8
+conda create -n optinist python=3.9
 conda activate optinist
 ```
 

diff --git a/docs/installation/users/windows_wsl.md b/docs/installation/users/windows_wsl.md
@@ -9,6 +9,7 @@
 WSL (Windows Subsystem for Linux) lets you run a Linux environment directly on Windows 10 and newer versions, without the need for a traditional virtual machine.
 
 - To install WSL:
+
   1. Open PowerShell or Windows Command Prompt as Administrator
   2. Run: `wsl --install`
   3. Open a new terminal and run: `wsl`
@@ -61,7 +62,7 @@ conda config --set channel_priority flexible
 ### Create Conda Environment
 
 ```bash
-conda create -n optinist python=3.8
+conda create -n optinist python=3.9
 conda activate optinist
 ```
 

diff --git a/frontend/build/asset-manifest.json b/frontend/build/asset-manifest.json
@@ -1,17 +1,17 @@
 {
   "files": {
-    "main.css": "/static/css/main.edcdbd9f.css",
-    "main.js": "/static/js/main.8ff79039.js",
+    "main.css": "/static/css/main.95e38137.css",
+    "main.js": "/static/js/main.24a5111e.js",
     "static/js/488.8edbc83a.chunk.js": "/static/js/488.8edbc83a.chunk.js",
     "static/media/logo.png": "/static/media/logo.e44efe3246aecc6d6219.png",
     "static/media/index.cjs": "/static/media/index.d64cca1358b36db061fb.cjs",
     "index.html": "/index.html",
-    "main.edcdbd9f.css.map": "/static/css/main.edcdbd9f.css.map",
-    "main.8ff79039.js.map": "/static/js/main.8ff79039.js.map",
+    "main.95e38137.css.map": "/static/css/main.95e38137.css.map",
+    "main.24a5111e.js.map": "/static/js/main.24a5111e.js.map",
     "488.8edbc83a.chunk.js.map": "/static/js/488.8edbc83a.chunk.js.map"
   },
   "entrypoints": [
-    "static/css/main.edcdbd9f.css",
-    "static/js/main.8ff79039.js"
+    "static/css/main.95e38137.css",
+    "static/js/main.24a5111e.js"
   ]
 }
diff --git a/frontend/build/index.html b/frontend/build/index.html
@@ -1 +1 @@
-<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.8ff79039.js"></script><link href="/static/css/main.edcdbd9f.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
+<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.24a5111e.js"></script><link href="/static/css/main.95e38137.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
diff --git a/frontend/build/static/css/main.95e38137.css b/frontend/build/static/css/main.95e38137.css
diff --git a/frontend/build/static/css/main.95e38137.css.map b/frontend/build/static/css/main.95e38137.css.map
diff --git a/frontend/build/static/css/main.edcdbd9f.css b/frontend/build/static/css/main.edcdbd9f.css
diff --git a/frontend/build/static/css/main.edcdbd9f.css.map b/frontend/build/static/css/main.edcdbd9f.css.map
diff --git a/frontend/build/static/js/main.24a5111e.js b/frontend/build/static/js/main.24a5111e.js
diff --git a/...ld/static/js/main.c3882d38.js.LICENSE.txt → ...ld/static/js/main.24a5111e.js.LICENSE.txt b/...ld/static/js/main.c3882d38.js.LICENSE.txt → ...ld/static/js/main.24a5111e.js.LICENSE.txt
@@ -71,6 +71,16 @@ object-assign
  * LICENSE file in the root directory of this source tree.
  */
 
+/**
+ * @license React
+ * react-is.production.js
+ *
+ * Copyright (c) Meta Platforms, Inc. and affiliates.
+ *
+ * This source code is licensed under the MIT license found in the
+ * LICENSE file in the root directory of this source tree.
+ */
+
 /**
  * @license React
  * react-is.production.min.js
@@ -113,26 +123,26 @@ object-assign
 
 /**
  * @license React
- * use-sync-external-store-shim.production.min.js
+ * use-sync-external-store-shim.production.js
  *
- * Copyright (c) Facebook, Inc. and its affiliates.
+ * Copyright (c) Meta Platforms, Inc. and affiliates.
  *
  * This source code is licensed under the MIT license found in the
  * LICENSE file in the root directory of this source tree.
  */
 
 /**
  * @license React
- * use-sync-external-store-shim/with-selector.production.min.js
+ * use-sync-external-store-shim/with-selector.production.js
  *
- * Copyright (c) Facebook, Inc. and its affiliates.
+ * Copyright (c) Meta Platforms, Inc. and affiliates.
  *
  * This source code is licensed under the MIT license found in the
  * LICENSE file in the root directory of this source tree.
  */
 
 /**
- * @remix-run/router v1.21.0
+ * @remix-run/router v1.21.1
  *
  * Copyright (c) Remix Software Inc.
  *
@@ -148,7 +158,7 @@ object-assign
  */
 
 /**
- * React Router DOM v6.28.0
+ * React Router DOM v6.28.2
  *
  * Copyright (c) Remix Software Inc.
  *
@@ -159,7 +169,7 @@ object-assign
  */
 
 /**
- * React Router v6.28.0
+ * React Router v6.28.2
  *
  * Copyright (c) Remix Software Inc.
  *

diff --git a/frontend/build/static/js/main.24a5111e.js.map b/frontend/build/static/js/main.24a5111e.js.map
diff --git a/frontend/build/static/js/main.8ff79039.js b/frontend/build/static/js/main.8ff79039.js
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.8ff79039.js"></script><link href="/static/css/main.edcdbd9f.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>
		<!doctype html><html lang="en"><head><meta charset="utf-8"/><link rel="icon" href="/static/favicon.ico"/><meta name="viewport" content="width=device-width,initial-scale=1"/><meta name="theme-color" content="#000000"/><meta name="description" content="Web site created using create-react-app"/><link rel="manifest" href="/static/manifest.json"/><title>OptiNiSt</title><script defer="defer" src="/static/js/main.24a5111e.js"></script><link href="/static/css/main.95e38137.css" rel="stylesheet"></head><body><noscript>You need to enable JavaScript to run this app.</noscript><div id="root"></div></body></html>