fill-voids

library2.1.2pypypiunverified

Fill voids (holes) in 3D binary images (numpy arrays) using a flood-fill algorithm. Fast and memory-efficient algorithm for hole filling in labeled or binary volumes. Current version 2.1.2, released Oct 2024. Releases are occasional, with breaking changes in the past (e.g., v2.0).

data ai-ml

pip install fill-voids

github ↗package ↗

INSTALL

IMPORT

SIG · FILL-VOIDS

fill-voids

datapythonv2.1.2

Install

4.0s avg

Import

—

Disk

123MB

Pass rate

5/ 10

Env Coverage5 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.1.2 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.910 runs

build_error

glibc

py 3.10–3.910 runs

installs and imports cleanly · install 4.0s · import 0.000s · 121MB

123MB installed

● package 123MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

fill_voids

✓ from fill_voids import fill_voids

✗ from fill_voids import fill_voids

Fills holes in a 3D binary numpy array.

import numpy as np from fill_voids import fill_voids # Create a binary volume with a hole image = np.ones((5,5,5), dtype=bool) image[2:4, 2:4, 2:4] = False # hole # Fill the hole filled = fill_voids(image) print(filled.all()) # Should be True

Debug

Known issues

breakingIn v2.0, the main function was renamed from 'fill' to 'fill_voids'. Code using 'from fill_voids import fill' will break.

fix

Update import to 'from fill_voids import fill_voids' and call fill_voids() instead of fill().

affects: <2.0

breakingIn v2.0, the library no longer accepts 2D arrays by default. Use fill_voids with 3D or upgrade to handle 2D via a workaround (e.g., add a dummy axis).

fix

Ensure input is 3D (shape (Z, Y, X)). For 2D, reshape: image_3d = image[np.newaxis, ...]; then fill; then squeeze.

affects: <2.0

gotchafill_voids fills fully enclosed background regions only. It does not fill holes touching the image border by default.

fix

Pad the array with a border of foreground voxels before filling, or use the 'in_place' argument if available.

affects: all

gotchaThe function modifies the input array in place if in_place=True (default False). Setting in_place=True can save memory but alters the original array.

fix

Use in_place=False (default) to preserve input; copy the array first if needed.

affects: >=2.0

Upgrade

Version history

2.1.2latest on PyPI · released Apr 30, 2026

Audit

Dependencies

numpyrequiredCore dependency for array manipulation.

scipyoptionalOptional; used for some fast watershed operations.

fastremapoptionalOptional; needed for remapping after filling.

Agent activity

9 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/seung-lab/fill_voids ↗

packagehttps://pypi.org/project/fill-voids/ ↗