| Name | bellavista JSON |
| Version |
0.0.2
JSON |
| download |
| home_page | None |
| Summary | Python package for interactive visualization of imaging-based spatial transcriptomics. |
| upload_time | 2024-09-30 23:53:07 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License Copyright (c) 2024 Annabelle Coles, Pallav Kosuri 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 |
spaital transcriptomics
visualization
napari
python
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Bella Vista
<p align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="https://github.com/pkosurilab/BellaVista/blob/main/images/bellavista_figure_darkmode.png?raw=true" width="900">
<img alt="Bella Vista workflow" src="https://github.com/pkosurilab/BellaVista/blob/main/images/bellavista_figure.png?raw=true" width="900">
</picture>
</p>
<p align="center">
Bella Vista enables visualization of imaging-based spatial transcriptomics data. It is an open-source Python package currently supporting 10x Genomics Xenium, Vizgen MERSCOPE, and custom (home-built) MERFISH datasets, utilizing [napari](https://napari.org/) for interactive data exploration. We developed Bella Vista to help the spatial transcriptomics community explore their data and create reproducible paper-ready figures. For more information, see our [documentation website](https://bellavista.readthedocs.io/en/latest/).
## Installation
The following instructions require that you have [Anaconda](https://www.anaconda.com/) installed.
- It is recommended to create an Anaconda virtual environment to prevent conflicting package dependencies.
- The package can be installed from PyPI via [pip](https://pypi.org/project/pip/) (recommended) or from the [GitHub repository](https://github.com/pkosurilab/BellaVista).
- Bella Vista requires python 3.9 or above.
Create and activate a new virtual environment:
```
conda create -n bellavista_env python
conda activate bellavista_env
```
Install via pip:
```
pip install bellavista
```
---
## Quickstart (with sample data)
Below is a short tutorial for loading Bella Vista with sample Xenium data.
1. Download sample data: [Xenium mouse brain dataset (Replicate 3)](https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-replicates-1-standard)
- To download the dataset, 10x Genomics may ask you to fill out a questionnaire.
- Unzip the downloaded zip file. This will create a folder named "Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs".
- Take note of your local path to this folder, as you will need this path when running Bella Vista.
<img src="https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_testdata_location.png?raw=true" alt="Xenium sample data website location" width="600" />
2. Run Bella Vista from the command line with the Xenium sample data:
- Note: Before running this command, replace "/path/to/" with the actual path to the Xenium sample data folder.
```
bellavista --xenium-sample /path/to/Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs
```
<br/>
> **NOTE:**
>
> It will take a few minutes to create the required data files.
<br/>
Once successfully loaded, you should see the message `Data Loaded!` in the terminal.
A napari window should appear displaying the data similar to the image below:
<br/>
<img src="https://github.com/pkosurilab/BellaVista/blob/updates/misc-changes/images/xenium_initial.png?raw=true" alt="Initial napari load page"/>
<br/>
> **TIP:**
>
> This is a large dataset, so if the program encounters a memory-related error, try visualizing a smaller subset of the data:
> ```
> bellavista --xenium-sample-lite /path/to/Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs
>```
>
Now, you can interactively move around the napari canvas to explore the data!\
Try zooming in & out, toggling layers on & off to see different spatial patterns:
<br/>
<img src="https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_brain_position_0_select.png?raw=true" alt="zoom out screenshot" />
<br/><br/>
<img src="https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_brain_position_1.png?raw=true" alt="zoom in screenshot" />
<br/><br/>
<img src="https://github.com/pkosurilab/BellaVista/blob/updates/misc-changes/images/xenium_brain_position_2_cellbounds.png?raw=true" alt="zoom in cellbounds screenshot" />
<br/>
> **TIP:**
>
> To visualize a single layer, and hide all other layers, `Option/Alt-click` on the visibility button (the eye, to the left of the layer name).
>
> Check out our [FAQ](https://bellavista.readthedocs.io/en/latest/faq.html#helpful-napari-tips) on the documentation website for more tips!
> **NOTE:**
>
> Gene colors are assigned randomly every time Bella Vista is launched. So, the gene colors displayed in your window will be different from the image above. Refer to our [FAQ](https://bellavista.readthedocs.io/en/latest/faq.html#helpful-napari-tips) on the documentation website for information on how to configure gene colors and other customizable visualization options.
>
> To reproduce the same colors every time you launch Bella Vista, refer to the [figure guide](https://bellavista.readthedocs.io/en/latest/figure_guide.html) on the documentation website.
<br/>
For an exact reproduction of the screenshots above, please refer to the figure guide: [Reproducing sample figures (Xenium)](https://bellavista.readthedocs.io/en/latest/figure_guide.html#reproducing-sample-figures-xenium) on the documentation website.
### To run Bella Vista with your own data, refer to the tutorials on the [documentation website](https://bellavista.readthedocs.io/en/latest/tutorials.html).
Raw data
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"description": "# Bella Vista\n\n<p align=\"center\">\n <picture>\n <source media=\"(prefers-color-scheme: dark)\" srcset=\"https://github.com/pkosurilab/BellaVista/blob/main/images/bellavista_figure_darkmode.png?raw=true\" width=\"900\">\n <img alt=\"Bella Vista workflow\" src=\"https://github.com/pkosurilab/BellaVista/blob/main/images/bellavista_figure.png?raw=true\" width=\"900\">\n </picture>\n</p>\n<p align=\"center\">\n\nBella Vista enables visualization of imaging-based spatial transcriptomics data. It is an open-source Python package currently supporting 10x Genomics Xenium, Vizgen MERSCOPE, and custom (home-built) MERFISH datasets, utilizing [napari](https://napari.org/) for interactive data exploration. We developed Bella Vista to help the spatial transcriptomics community explore their data and create reproducible paper-ready figures. For more information, see our [documentation website](https://bellavista.readthedocs.io/en/latest/).\n\n## Installation\nThe following instructions require that you have [Anaconda](https://www.anaconda.com/) installed.\n- It is recommended to create an Anaconda virtual environment to prevent conflicting package dependencies. \n- The package can be installed from PyPI via [pip](https://pypi.org/project/pip/) (recommended) or from the [GitHub repository](https://github.com/pkosurilab/BellaVista).\n- Bella Vista requires python 3.9 or above.\n\nCreate and activate a new virtual environment:\n\n```\nconda create -n bellavista_env python\nconda activate bellavista_env\n```\n\nInstall via pip:\n```\npip install bellavista\n```\n\n---\n## Quickstart (with sample data)\n\nBelow is a short tutorial for loading Bella Vista with sample Xenium data.\n\n1. Download sample data: [Xenium mouse brain dataset (Replicate 3)](https://www.10xgenomics.com/datasets/fresh-frozen-mouse-brain-replicates-1-standard)\n\n - To download the dataset, 10x Genomics may ask you to fill out a questionnaire.\n - Unzip the downloaded zip file. This will create a folder named \"Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs\".\n - Take note of your local path to this folder, as you will need this path when running Bella Vista.\n\n<img src=\"https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_testdata_location.png?raw=true\" alt=\"Xenium sample data website location\" width=\"600\" />\n\n\n2. Run Bella Vista from the command line with the Xenium sample data:\n\n - Note: Before running this command, replace \"/path/to/\" with the actual path to the Xenium sample data folder.\n\n```\nbellavista --xenium-sample /path/to/Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs\n```\n\n<br/>\n\n> **NOTE:**\n>\n> It will take a few minutes to create the required data files.\n\n<br/>\nOnce successfully loaded, you should see the message `Data Loaded!` in the terminal. \n\nA napari window should appear displaying the data similar to the image below:\n\n<br/>\n<img src=\"https://github.com/pkosurilab/BellaVista/blob/updates/misc-changes/images/xenium_initial.png?raw=true\" alt=\"Initial napari load page\"/>\n\n<br/>\n\n> **TIP:**\n>\n> This is a large dataset, so if the program encounters a memory-related error, try visualizing a smaller subset of the data:\n> ```\n> bellavista --xenium-sample-lite /path/to/Xenium_V1_FF_Mouse_Brain_MultiSection_3_outs\n>```\n> \n\nNow, you can interactively move around the napari canvas to explore the data!\\\nTry zooming in & out, toggling layers on & off to see different spatial patterns:\n\n<br/>\n\n<img src=\"https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_brain_position_0_select.png?raw=true\" alt=\"zoom out screenshot\" />\n<br/><br/>\n<img src=\"https://github.com/pkosurilab/BellaVista/blob/main/images/xenium_brain_position_1.png?raw=true\" alt=\"zoom in screenshot\" />\n<br/><br/>\n<img src=\"https://github.com/pkosurilab/BellaVista/blob/updates/misc-changes/images/xenium_brain_position_2_cellbounds.png?raw=true\" alt=\"zoom in cellbounds screenshot\" />\n\n<br/>\n\n> **TIP:**\n>\n> To visualize a single layer, and hide all other layers, `Option/Alt-click` on the visibility button (the eye, to the left of the layer name). \n>\n> Check out our [FAQ](https://bellavista.readthedocs.io/en/latest/faq.html#helpful-napari-tips) on the documentation website for more tips!\n\n> **NOTE:**\n>\n> Gene colors are assigned randomly every time Bella Vista is launched. So, the gene colors displayed in your window will be different from the image above. Refer to our [FAQ](https://bellavista.readthedocs.io/en/latest/faq.html#helpful-napari-tips) on the documentation website for information on how to configure gene colors and other customizable visualization options.\n>\n> To reproduce the same colors every time you launch Bella Vista, refer to the [figure guide](https://bellavista.readthedocs.io/en/latest/figure_guide.html) on the documentation website.\n<br/>\n\nFor an exact reproduction of the screenshots above, please refer to the figure guide: [Reproducing sample figures (Xenium)](https://bellavista.readthedocs.io/en/latest/figure_guide.html#reproducing-sample-figures-xenium) on the documentation website.\n\n\n### To run Bella Vista with your own data, refer to the tutorials on the [documentation website](https://bellavista.readthedocs.io/en/latest/tutorials.html).\n",
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