README.md

bioimage-cpp

Stand-alone implementation of image analysis and segmentaton functionality in C++ with minimal python bindings.

bioimage-cpp is a small C++/Python package for dependency-light bioimage-analysis algorithms that are difficult to install from larger C++ libraries. It exposes NumPy-based Python APIs backed by a focused C++20 core.

Install

python -m pip install bioimage-cpp

Build from source

python -m pip install -v ".[test]"
pytest -q

Example

import numpy as np
import bioimage_cpp as bic

labels = np.array([1, 3, 2, 1], dtype=np.uint64)
relabeling = {1: 10, 2: 20, 3: 30}

out = bic.utils.take_dict(relabeling, labels)
# array([10, 30, 20, 10], dtype=uint64)

affinities = np.ones((2, 4, 4), dtype=np.float32)
offsets = [[0, 1], [1, 0]]

segmentation = bic.segmentation.mutex_watershed(
    affinities,
    offsets,
    number_of_attractive_channels=2,
)

graph = bic.graph.UndirectedGraph.from_edges(4, [[0, 1], [1, 2], [2, 3]])
graph.find_edge(2, 1)
# 1

grid = bic.graph.grid_graph((64, 64))
grid.number_of_edges
# 8064

edge_weights = bic.graph.grid_boundary_features(grid, boundary_map)
local_weights, valid_edges, lifted_uvs, lifted_weights, offset_ids = (
    bic.graph.grid_affinity_features_with_lifted(grid, affinities, offsets)
)

Scope

The project is not a compatibility layer for nifty, vigra, or other large libraries. It keeps I/O and heavy dependencies out of the C++ core; callers should use existing Python packages for file formats and pass NumPy arrays into bioimage-cpp.