Alternatives and similar repositories for microaligner

Users that are interested in microaligner are comparing it to the libraries listed below

• ilastik / ilastik-napari

  View on GitHub
  ilastik plugin for napari
  ☆14Dec 15, 2025Updated last month
• constantinpape / pybdv

  View on GitHub
  python tools for BigDataViewer
  ☆22Dec 29, 2024Updated last year
• multiview-stitcher / napari-stitcher

  View on GitHub
  A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher
  ☆17Jul 7, 2025Updated 7 months ago
• YeoLab / bento-tools

  View on GitHub
  A Python toolkit for subcellular analysis of spatial transcriptomics data
  ☆86Nov 16, 2025Updated 2 months ago
• hanjinliu / impy

  View on GitHub
  Speed up coding/extending image analysis in Python.
  ☆37Jan 20, 2026Updated 3 weeks ago
• QI2lab / OPM

  View on GitHub
  Archived: control, reconstruction, and analysis code for oblique plane microscopy.
  ☆22Apr 1, 2025Updated 10 months ago
• spatial-image / multiscale-spatial-image

  View on GitHub
  Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
  ☆55Nov 13, 2025Updated 3 months ago
• lukasz-migas / napari-plot

  View on GitHub
  1d plotting in napari-based canvas.
  ☆25Updated this week
• Gubra-ApS / LSFM-mouse-brain-atlas

  View on GitHub
  ☆19Apr 6, 2022Updated 3 years ago
• NicoKiaru / ABBA-Python

  View on GitHub
  How to use Aligning Big Brains and Atlases with Python
  ☆14May 3, 2023Updated 2 years ago
• spatial-image / spatial-image

  View on GitHub
  A multi-dimensional spatial image data structure for scientific Python.
  ☆44Aug 8, 2025Updated 6 months ago
• Euro-BioImaging / BatchConvert

  View on GitHub
  A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, i…
  ☆25Mar 14, 2025Updated 11 months ago
• ome / ome-zarr-py

  View on GitHub
  Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
  ☆224Updated this week
• dmattek / dzPlateViewer

  View on GitHub
  Deep Zoom Plate Viewer for microscopy images
  ☆18Feb 3, 2026Updated last week
• scverse / spatialdata-io

  View on GitHub
  ☆88Updated this week
• matplotlib / napari-matplotlib

  View on GitHub
  Linking napari layers with Matplotlib plots
  ☆43Feb 2, 2026Updated last week
• tlambert03 / napari-ndtiffs

  View on GitHub
  A napari plugin to load & deskew folders of lattice light sheet TIFFs
  ☆13Jan 5, 2026Updated last month
• fcaprile / PyFocus

  View on GitHub
  This is PyFocus, a Python package that provides high-level functions and an user interface to perform full vectorial calculations of the …
  ☆16Oct 31, 2023Updated 2 years ago
• hinderling / napari_pixel_classifier

  View on GitHub
  An Ilastik-like interactive pixel classifier.
  ☆16Sep 5, 2024Updated last year
• BBQuercus / deepBlink

  View on GitHub
  Threshold independent detection and localization of diffraction-limited spots.
  ☆38Nov 1, 2022Updated 3 years ago
• haesleinhuepf / napari-assistant

  View on GitHub
  ☆33May 2, 2025Updated 9 months ago
• AdaptiveParticles / pyapr

  View on GitHub
  Content-adaptive storage and processing of large volumetric microscopy data using the Adaptive Particle Representation (APR)
  ☆21Aug 21, 2024Updated last year
• theislab / troutpy

  View on GitHub
  Package for the analysis of Transcripts outside segmented cells in ST data
  ☆26Updated this week
• guiwitz / napari-annotation-project

  View on GitHub
  A minimalistic napari plugin to create and save regions of interest and annotations on series of images
  ☆18Apr 8, 2025Updated 10 months ago
• yapic / yapic

  View on GitHub
  Yet Another Pixel Classifier (based on deep learning)
  ☆36Jun 27, 2024Updated last year
• stardist / augmend

  View on GitHub
  simple package for augmentation of n-dimensional arrays
  ☆34Aug 10, 2023Updated 2 years ago
• multiview-stitcher / multiview-stitcher

  View on GitHub
  A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.
  ☆105Updated this week
• vitessce / vitessce-python

  View on GitHub
  Python API and Jupyter widget for Vitessce
  ☆61Feb 5, 2026Updated last week
• clEsperanto / pyclesperanto_prototype

  View on GitHub
  GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
  ☆238Feb 21, 2025Updated 11 months ago
• brainglobe / brainglobe-registration

  View on GitHub
  Registration to BrainGlobe atlases in napari using Elastix
  ☆29Updated this week
• BiAPoL / napari-clusters-plotter

  View on GitHub
  A napari plugin for clustering objects according to their properties.
  ☆90Jan 26, 2026Updated 2 weeks ago
• SlicerMorph / S_2019

  View on GitHub
  Lectures, labs and all documents associated with 3D Morphometrics workshop at FHL (Summer 2019)
  ☆14Feb 6, 2020Updated 6 years ago
• hanjinliu / magic-class

  View on GitHub
  Generate multifunctional and macro recordable GUIs from Python classes
  ☆45Nov 16, 2025Updated 2 months ago
• wanglab-broad / CAST

  View on GitHub
  CAST package
  ☆42Oct 26, 2024Updated last year
• constantinpape / cluster_tools

  View on GitHub
  Distributed segmentation for bio-image-analysis
  ☆41Jan 18, 2026Updated 3 weeks ago
• scverse / napari-spatialdata

  View on GitHub
  Interactive visualization of spatial omics data
  ☆75Feb 1, 2026Updated last week
• fractal-analytics-platform / fractal-tasks-core

  View on GitHub
  Main tasks for the Fractal analytics platform
  ☆23Feb 5, 2026Updated last week
• angelolab / ark-analysis

  View on GitHub
  Integrated pipeline for multiplexed image analysis
  ☆102Jan 7, 2026Updated last month
• georgeoshardo / SyMBac

  View on GitHub
  Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
  ☆22Jul 23, 2025Updated 6 months ago