3D segmentation for cells and organoids of 3D multichannel images
☆32Jun 23, 2026Updated this week
Alternatives and similar repositories for 3DcellScope
Users that are interested in 3DcellScope are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An introduction to OME-Zarr for big bioimaging data☆27Jun 2, 2026Updated 3 weeks ago
- A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processi…☆29Jun 16, 2026Updated last week
- Rust extension module for FIJI-like colormapping and channel blending☆21Updated this week
- Use Napari Viewer to display CZI images☆11May 25, 2022Updated 4 years ago
- SuperCell for Cytometry data☆13Oct 14, 2025Updated 8 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- Lab for quantitative bioimage analysis experiments in Python☆20Feb 16, 2026Updated 4 months ago
- ☆23Mar 22, 2023Updated 3 years ago
- Sub-cellular spatial transcriptomics Cell Segmentation☆70Oct 1, 2023Updated 2 years ago
- R package: ConDecon is a clustering-independent deconvolution method for estimating cell abundances in bulk tissues using single-cell RNA…☆14Oct 17, 2024Updated last year
- ☆29Apr 1, 2025Updated last year
- Publically accessible code for DIISCO method☆13Oct 15, 2025Updated 8 months ago
- This repository provides a collection of tools to simplify reading CZI (Carl Zeiss Image) pixel and metadata in Python.☆22May 22, 2026Updated last month
- Imaris file format reader☆15Aug 20, 2025Updated 10 months ago
- a deep generative model for single-cell survival analysis☆26Dec 2, 2025Updated 6 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Scientific Dataset Quality Control and Data Exploration Tool☆23Jun 19, 2026Updated last week
- RAnking Markers for CEll Segmentation☆12Feb 22, 2022Updated 4 years ago
- A computational tool for identification of 3D multi-modal spatial neighborhoods☆15Aug 1, 2025Updated 10 months ago
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆33Aug 20, 2025Updated 10 months ago
- Toolkit for metacell analysis☆24Aug 8, 2024Updated last year
- A short course exploring several fun and useful notebooks and Napari widgets for deep learning with SAM, Cellpose, Stardist and friends.☆19Dec 9, 2025Updated 6 months ago
- Segment images utilizing pre-trained neural networks as feature extractors☆52Updated this week
- Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.☆56Nov 13, 2025Updated 7 months ago
- QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis☆35Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.☆71Updated this week
- Flow2Spatial reconstructs spatial proteomics through transfer learning.☆25May 16, 2025Updated last year
- Python scripts library for Aivia. Ask your questions on the forum >>☆14Updated this week
- Dataset EXploration & Processing☆33May 11, 2023Updated 3 years ago
- A template repo used to make new napari plugins☆39Updated this week
- A framework for easy application of established machine learning techniques on large, multi-dimensional images.☆60Apr 24, 2026Updated 2 months ago
- https://sparrow-pipeline.readthedocs.io/en/latest/☆33Jun 22, 2026Updated last week
- A Python toolbox for aligning / fusing / stitching large multi-view / multi-positioning image datasets in 2-3D.☆119Jun 22, 2026Updated last week
- A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks☆121May 22, 2026Updated last month
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Scatterbar - data visualization for proportional data across many spatially resolved coordinates☆12Mar 3, 2025Updated last year
- Main tasks for the Fractal analytics platform