semvec/pypi-packages huggingface dataset:
nuclear-shape 0.1.1
Python package for analysing nuclear shape from 3D-genome models generated from Hi-C data.
License: MIT
Requires Python: >=3.9

# nuclear_shape

A small Python library for analysing nuclear shape from 3D‑genome models (Chrom3D `.cmm` files).  
Includes ellipsoid fitting, PCA, basic shape metrics, and simple plotting/rendering.

## Installation

```bash
pip install nuclear_shape
```


## Basic Usage

```python
from nuclear_shape import NuclearShape

shape = NuclearShape("path/to/file.cmm")

shape.ellipsoid_fit()
shape.ellipsoid_inner()
shape.ellipsoid_outer()
shape.compute_pca()

shape.print_metrics()
shape.plot("sphericity", show=True)
shape.render("ellipsoid", show=True)
```

## Example Data
An example .cmm file and a test script are included:

```code
test/example_real_data_0.cmm
python test/test.py
```

## License
MIT License
segtraq 0.0.3
SegTraQ - A Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.
License: MIT
Requires Python: >=3.11

# SegTraQ

[![PyPI version](https://badge.fury.io/py/segtraq.svg)](https://badge.fury.io/py/segtraq)

> ⚠️ Note: SegTraQ is under active development. 
> Features, interfaces, and functionality may change in upcoming releases. 
> SegTraQ currently supports imaging-based spatial transcriptomics data only. 
> Support for sequencing-based spatial transcriptomics is under development and will be included in a future release.
> To install the latest development version, run `pip install git+https://github.com/LazDaria/SegTraQ`.

SegTraQ (**Seg**mentation and **Tra**nscript Assignment **Q**uality Control) is a Python toolkit for quantitative and visual quality control of segmentation and transcript assignment in spatial omics data.

## Getting Started
Please refer to the [documentation](https://lazdaria.github.io/SegTraQ) for details on the API and tutorials.

## Installation

To install `SegTraQ`, first create a python environment and install the package using 

```
pip install segtraq
```

The installation of the package should take less than a minute.

## System Requirements
### Hardware Requirements
`SegTraQ` requires only a standard computer with enough RAM to support the in-memory operations.

### Software Requirements
`SegTraQ` depends on the following packages:
```
scanpy
spatialdata
geopandas
igraph
rtree
rasterio
squidpy
anndata
ovrlpy
```