Metadata-Version: 2.4
Name: HiVis
Version: 0.8.1
Summary: A user friendly tool for working with VisiumHD data
Home-page: https://github.com/roynov01/HiVis
Author: Roy Novoselsky
Author-email: Roy Novoselsky <roy.novoselsky@weizmann.ac.il>
License: The MIT License (MIT)
        
        Copyright (c) 2025 Roy Novoselsky.
        
        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
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Project-URL: Home, https://github.com/roynov01/HiVis
Project-URL: Documentation, https://hivis.readthedocs.io/en/latest/
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2.1.3
Requires-Dist: scipy>=1.15.2
Requires-Dist: matplotlib>=3.10.1
Requires-Dist: pandas>=2.2.3
Requires-Dist: seaborn>=0.13.2
Requires-Dist: scanpy==1.11.0
Requires-Dist: anndata>=0.11.3
Requires-Dist: adjustText
Requires-Dist: pyarrow>=19.0.1
Requires-Dist: pillow>=11.1.0
Requires-Dist: tqdm>=4.67.1
Requires-Dist: shapely>=2.0.7
Requires-Dist: geopandas>=1.0.1
Requires-Dist: dill>=0.3.9
Requires-Dist: tifffile>=2025.3.13
Requires-Dist: statsmodels>=0.14.4
Requires-Dist: scikit-learn>=1.5.2
Dynamic: author
Dynamic: home-page
Dynamic: license-file
Dynamic: requires-python
Dynamic: summary

**HiVis** is associated with the following manuscript: [Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics](https://www.biorxiv.org/content/10.1101/2025.09.07.674688v1)

# HD Integrated Visium Interactive Suite (HiVis)
* **HiVis** is a user-friendly Python tool for analyzing  
  [10X VisiumHD](https://www.10xgenomics.com/products/spatial-gene-expression) data,  
  supporting both H&E and immunofluorescence experiments.
* **HiVis** is built on top of [AnnData](https://anndata.readthedocs.io/en/latest/), 
integrating seamlessly with other spatial transcriptomics tools such as
 [Scanpy](https://scanpy.readthedocs.io/en/stable/) and 
 [Squidpy](https://squidpy.readthedocs.io/en/stable/).  
* **HiVis** provides extensive data visualization with fully customizable plots. 
Plots are created using *matplotlib*, allowing stacking and further customization.  
* **HiVis** works with 
[QuPath](https://qupath.readthedocs.io/en/stable/)
to enable easy manual annotation, pixel classification, and single-cell segmentation using
 [Stardist](https://github.com/stardist/stardist/) and 
 [Cellpose](https://github.com/MouseLand/cellpose).
 It links bins and single-cell objects, facilitating seamless information exchange across levels.  

![](docs/HiVis.png)

## Getting started
### Installation

To avoid dependency conflicts, we recommend the use of a 
dedicated 
[conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) 
environment.  In a terminal run the command:

```bash
conda create -n HiVis python=3.12
conda activate HiVis
```

We recommend two options to then install HiVis in your virtual environment.

Use the package manager [pip](https://pypi.org/project/HiVis/) to install HiVis. 
In a terminal run the command:

```bash
pip install HiVis
```

Or clone the project's [Github repository](https://github.com/roynov01/HiVis) 
and install it manually with the following commands:

```bash
git clone git@github.com:roynov01/HiVis.git
cd HiVis
pip install .
```

To use Qupath features, such as manual annotations and pixel classifiers, download and install 
[QuPath](https://qupath.github.io/) (>= 0.5.1).

To perform cell segmentation in QuPath, download and install [Stardist](https://github.com/qupath/qupath-extension-stardist) 
and/or [Cellpose](https://github.com/BIOP/qupath-extension-cellpose) extensions for QuPath.


### Usage and Documentation
Please refer to the [demo notebooks](https://github.com/roynov01/HiVis/tree/main/tutorials).

For QuPath, please refer to the [tutorial](https://github.com/roynov01/HiVis/tree/main/QuPath).

Function docstrings are available on [ReadTheDocs](https://hivis.readthedocs.io/en/latest/).

## Contact
Bug report/feature request via the [GitHub issue tracker](https://github.com/roynov01/HiVis/issues).

## Citation
Novoselsky R, Golani O, Barkai T, Kedmi M, Goliand I, Fine M, Kent I, Nachmany I, Itzkovitz S. *Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics*. *BioRxiv*, 2025.

