Euro-BioImaging / BatchConvertLinks
A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.
☆24Updated 8 months ago
Alternatives and similar repositories for BatchConvert
Users that are interested in BatchConvert are comparing it to the libraries listed below
Sorting:
- Ngio is a Python library to streamline OME-Zarr image analysis workflows.☆34Updated this week
- python tools for BigDataViewer☆22Updated 11 months ago
- Browse your OMERO database from within napari.☆39Updated last week
- A napari plugin for zarr backed OME-NGFF images☆42Updated last week
- Visualizing feature measurements on label images in napari☆10Updated last year
- A 3D interactivity toolbox for napari☆37Updated 5 months ago
- A napari plugin for stitching large multi-positioning datasets in 2/3D+t using multiview-stitcher☆16Updated 5 months ago
- ☆25Updated 2 years ago
- A module with convenience functions for writing Python code that interacts with OMERO.☆46Updated last week
- native Python dataclasses for the OME data model☆64Updated last week
- A toolbox for registering / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆95Updated this week
- Accelerated Pixel and Object Classifiers (APOC)☆58Updated 4 months ago
- GIve easy, high-level access to ome-zarr fileset☆22Updated 2 months ago
- Resources for teaching/preparing to teach bioimage analysis☆58Updated 2 weeks ago
- GPU-accelerated, OpenCL-based Random Forest Classifiers for pixel and labeled object classification in napari.☆45Updated 7 months ago
- A place to collect information used in lectures, demos, workshops, etc.☆17Updated last year
- An automated point-set based registration algorithm for correlative light and electron microscopy (CLEM)☆19Updated last month
- ☆22Updated 5 months ago
- ilastik plugin for napari☆14Updated 2 weeks ago
- Track and lineage visualization with btrack and Napari☆45Updated 2 months ago
- MultiModal Big Image Data Sharing and Exploration☆18Updated 2 years ago
- A minimal dependency napari plugin giving access to scikit-image functions☆23Updated 3 months ago
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆54Updated 3 weeks ago
- A minimal Python package for reading, writing and validating OME-Zarr (meta)data☆36Updated 3 weeks ago
- ☆15Updated last week
- Basic example of using OME-Zarr in a Nextflow pipeline☆19Updated 4 months ago
- Python libraries for loading, running and packaging bioimage.io models☆34Updated 2 weeks ago
- A short course exploring several fun and useful notebooks and Napari widgets for deep learning with SAM, Cellpose, Stardist and friends.☆18Updated 2 weeks ago
- Feature extraction for labeled objects in images using regionprops from scikit-image☆52Updated 7 months ago
- Command-line client for Fractal☆47Updated last week