https://github.com/aplbrain/reconstruct2stack

A Python library to convert Reconstruct or PyReconstruct segmentation contours to image mask stacks.
https://github.com/aplbrain/reconstruct2stack

Last synced: 10 months ago
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A Python library to convert Reconstruct or PyReconstruct segmentation contours to image mask stacks.

• Host: GitHub
• URL: https://github.com/aplbrain/reconstruct2stack
• Owner: aplbrain
• License: apache-2.0
• Created: 2023-03-05T03:26:19.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-03-06T18:58:56.000Z (over 3 years ago)
• Last Synced: 2025-03-15T09:22:39.894Z (over 1 year ago)
• Language: Python
• Size: 16.6 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# reconstruct2stack

[Reconstruct](https://github.com/SynapseWeb/PyReconstruct) is a connectomics segmentation and annotation tool. Reconstruct exports its annotations in the form of JSON-encoded contours, in a .jser file. This library reads .jser files and outputs a standard image-mask stack, in the form of a numpy array or image files.

## Installation

```bash

git clone https://github.com/aplbrain/reconstruct2stack

cd reconstruct2stack

poetry install

```

## Usage

```python

from reconstruct2stack import jser_to_image_stack

jser_to_image_stack(

    "my-series.jser",

    "segmentation-stack/",

    (8192, 8192), # image size, in XY pixels

)

```

This library is a work in progress. More documentation will follow shortly.