wiggins-lab / SuperSegger
A completely automated MATLAB-based trainable image cell segmentation, fluorescence quantification and analysis suite, particularly well suited for high-throughput time lapse fluorescence microscopy of in vivo bacterial cells.
☆33Updated 4 years ago
Alternatives and similar repositories for SuperSegger:
Users that are interested in SuperSegger are comparing it to the libraries listed below
- Toolbox for the analysis of smFISH images.☆59Updated last year
- EASI-FISH analysis pipeline for spatial transcriptomics☆34Updated 5 months ago
- A self-explanatory, hands-on intro to bioimage analysis in python. Slightly outdated but still much liked by learners.☆97Updated 2 years ago
- AICS Segmentation (One-Way) Mirror☆45Updated 4 years ago
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆35Updated 3 years ago
- quantixed FIJI update site☆16Updated 3 months ago
- A module with convenience functions for writing Python code that interacts with OMERO.☆44Updated this week
- segmentation of rod-shaped bacteria☆15Updated 2 years ago
- Tool for precise, interactive, fast and scalable FISH spot detection☆49Updated 2 months ago
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆15Updated 4 years ago
- Image registration (alignment) software for large microscopy images☆25Updated last year
- Pure Python library for reading NIS Elements ND2 images and metadata☆47Updated 3 months ago
- Track and lineage visualization with btrack and Napari☆45Updated 6 months ago
- Graph-based Decoding for In Situ Sequencing☆10Updated 4 years ago
- SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.☆37Updated last year
- ABBA, controlled from python☆11Updated last month
- ☆10Updated 4 years ago
- Semi-manual alignment to reference templates (SMART): An open source pipeline in R for whole brain mapping☆14Updated 3 years ago
- Lectures for a napari training course☆50Updated last year
- Python nd2 reader based on the ND2 SDK☆17Updated 3 years ago
- An automatic deep learning algorithm for spot detection in fluorescence microscopy images.☆20Updated 3 months ago
- ☆28Updated 2 months ago
- Cell tracker designed for tracking intestinal organoids☆21Updated last week
- A scalable machine learning pipeline for probe specificity prediction.☆14Updated last year
- astir | Automated cell identity from single-cell multiplexed imaging and proteomics 🖥🔬✨☆52Updated 10 months ago
- NEUBIAS Academy @Home: Interactive Bioimage Analysis with Python and Jupyter☆62Updated last year
- Example vignette for dotdotdot software☆18Updated 4 years ago
- MS Word template for styling a manuscript for a bioRxiv submission☆38Updated 6 years ago
- A platform for compiling, analyzing, and exploring tracking data☆43Updated last month
- Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)☆37Updated 2 months ago