microscopestitching 0.0.1

Automatic merge/stitching of regular spaced images

Overview

This software aims to be a reliable way to stitch your microscope images. To get good results, a couple of assumptions should be true about your dataset:

• images are regular spaced

• images are of same size

• side by side images have translation only in one dimension

• (if not, check your scanning mirror rotation)

• scale in edge of images are constant

Installation

Install using pip…

pip install microscopestitching

Example

from microscopestitching import stitch
from skimage.io import imsave

images = []
for i in range(50):
    row = i // 10
    col = i % 10
    images.append(('%d.png' % i, row, col))

merged = stitch(images)
imsave('merged.png', merged)

See also this notebook.

API reference

API reference is at http://microscopestitching.rtfd.org.

Development

Install dependencies and link development version of microscopestitching to pip:

git clone https://github.com/arve0/microscopestitching
cd microscopestitching
pip install -r requirements.txt # install dependencies and microscopestitching-package

Testing

tox

Build documentation locally

To build the documentation:

pip install -r docs/requirements.txt
make docs