☆93Nov 5, 2025Updated 4 months ago
Alternatives and similar repositories for BaSiCPy
Users that are interested in BaSiCPy are comparing it to the libraries listed below
Sorting:
- This is the main repository for MemBrain v2. It includes MemBrain-seg, MemBrain-pick, MemBrain-stats, and several Napari tools.☆21Jan 29, 2025Updated last year
- A BaSiC Tool for Background and Shading Correction of Optical Microscopy Images☆65Mar 12, 2025Updated 11 months ago
- ☆16Feb 5, 2026Updated last month
- ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration☆165Feb 19, 2026Updated 2 weeks ago
- Ngio is a Python library to streamline OME-Zarr image analysis workflows.☆42Feb 23, 2026Updated last week
- A Python toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆106Feb 11, 2026Updated 3 weeks ago
- MIST-inspired microscope image stitching package☆80Jan 29, 2026Updated last month
- Piecewise alignment for layers of mosaics☆39Feb 18, 2026Updated 2 weeks ago
- A napari plugin for zarr backed OME-NGFF images☆45Updated this week
- Paint segmentations directly to on-disk/remote zarr arrays☆15Jun 26, 2024Updated last year
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆55Nov 13, 2025Updated 3 months ago
- Single cell Morphology Quality Control (coSMicQC)☆10Updated this week
- An introduction to OME-Zarr for big bioimaging data☆24Updated this week
- A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, i…☆28Mar 14, 2025Updated 11 months ago
- Image reading, metadata management, and image writing for Microscopy images in Python☆114Feb 25, 2026Updated last week
- Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.☆225Feb 23, 2026Updated last week
- A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data☆192Updated this week
- ☆36Mar 22, 2024Updated last year
- Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python☆221Dec 1, 2025Updated 3 months ago
- A relabeling tool for tiled segmentation with Dask☆17Sep 24, 2024Updated last year
- Experimental micro-service for implementing the Zarr spec over HTTP☆20Jan 19, 2026Updated last month
- A collection of Image Processing and Analysis (IPA) functions used at the Facility for Advanced Imaging and Microscopy (FAIM)☆19Updated this week
- Graph-based framework to manipulate and analyze cell lineages from cell tracking data☆24Updated this week
- A multi-dimensional spatial image data structure for scientific Python.☆44Aug 8, 2025Updated 6 months ago
- QuPath extension for Cellsparse☆19May 6, 2025Updated 10 months ago
- NGFF-Converter is a GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF☆35Nov 26, 2025Updated 3 months ago
- Official implementation of CytoSAE: Interpretable Cell Embeddings for Hematology☆22Jul 17, 2025Updated 7 months ago
- A basis for a napari plugin for manually correcting cell segmentation in 3D (z, y, x) or 4D (t, z, y, x) (virtual) arrays.☆10Updated this week
- membrane segmentation in 3D for cryo-ET☆86Feb 27, 2026Updated last week
- Find profile pairs and compute retrieval metrics between them.☆22Updated this week
- ☆19Updated this week
- Full-featured nd2 (Nikon NIS Elements) file reader for python. Outputs to numpy, dask, and xarray. Exhaustive metadata extraction☆76Feb 19, 2026Updated 2 weeks ago
- Weakly-supervised learning pipeline for histopathology images. Publications: Biomarker prediction in colorectal cancer (CRC)☆84Feb 6, 2024Updated 2 years ago
- a generalist algorithm for cellular segmentation with human-in-the-loop capabilities☆2,089Updated this week
- An Interactive Image Segmentation Filter for Multiplex Microscopy☆31Feb 12, 2026Updated 3 weeks ago
- Software for dynamic spherical harmonic analysis☆10May 1, 2020Updated 5 years ago
- native Python dataclasses for the OME data model☆65Feb 12, 2026Updated 3 weeks ago
- serve Zarr datasets via HTTP☆31Jun 12, 2023Updated 2 years ago
- BIOMERO.analyzer - A python library for easy connecting between OMERO (jobs) and a Slurm cluster☆24Feb 26, 2026Updated last week