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Automatic merge/stitching of regular spaced images

Project description

build-status-image pypi-version wheel


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


Install using pip

pip install microscopestitching


from microscopestitching import stitch
from 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 notebook examples.

API reference

API reference is at


Install dependencies and link development version of microscopestitching to pip:

git clone
cd microscopestitching
pip install -r requirements.txt # install dependencies and microscopestitching-package



Build documentation locally

To build the documentation:

pip install -r docs/requirements.txt
make docs

Project details

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microscopestitching-0.2.0.tar.gz (4.1 MB view hashes)

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