Metadata-Version: 2.1
Name: splinedist
Version: 0.1.0
Summary: splinedist
Home-page: https://github.com/uhlmanngroup/splinedist
Author: uhlmanngroup
Author-email: uhlmann@ebi.ac.uk
Keywords: splinedist
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: LICENSE_stardist.txt
Requires-Dist: stardist (==0.6.2)
Requires-Dist: tensorflow


# SplineDist: Automated Cell Segmentation with Spline Curves 

This repository contains the implementation of SplineDist, a machine learning framework for automated cell segmentation with spline curves.  The [manuscript](https://www.biorxiv.org/content/10.1101/2020.10.27.357640v1) is accepted at [ISBI 2021](https://biomedicalimaging.org/2021/). The code in its current state allows reproducing the paper experiments but is still in development. We are currently working to package it in a cleaned and optimized form. In the meantime, we encourage interested end-users to contact us for more information and assistance.


## Overview
SplineDist has been designed for performing instance segmentation in bioimages. Our method has been built by extending the popular [StarDist](https://arxiv.org/abs/1806.03535) framework. Our repository relies on the high-quality [StarDist](https://github.com/mpicbg-csbd/stardist) repository.  We encourage the user to explore StarDist repository for further details on the StarDist method.

While StarDist models objects with star-convex polygonal representation, SplineDist models objects as parametric spline curves. As our representation is more general, it allows to model non-star-convex objects as well, with the possibility of conducting further statistical shape analysis.


## Requirements 

1. Tensorflow

2. [StarDist 0.6.2](https://github.com/mpicbg-csbd/stardist) (can be installed with `pip` : `pip install stardist==0.6.2`)


## Walkthrough

Three walkthrough notebooks have been included in this repository for data-exploration, training, and inference tasks.


## Datasets

The synthetic dataset used in the SplineDist manuscript can be found [here](https://osf.io/z89pq/).This dataset contains synthetic images with mostly star-convex and some non-star convex cell-like objects. 
