Pinned Repositories
AIRLOCALIZE
Software for spot detection
bioanalyze-docker-images
Docker Images for Jupyterhub + Bioinformatics
DNAbarcodes
Simple generator of DNA barcodes for sequencing experiments
EASI-FISH
Tools and scripts for EASI-FISH image data analysis
elastix
Official elastix repository
FISHscale
Spatial analysis of FISH data
metacell
Metacell - Single-cell mRNA Analysis
postcode
Decoding of image-based spatial transcriptomics
qupath-extension-warpy
ImgLib2 RealTransform brought to QuPath
starfish
starfish: unified pipelines for image-based transcriptomics
lbgbox's Repositories
lbgbox/applied-bioinformatics-iab2
An Introduction to Applied Bioinformatics, 2nd Edition
lbgbox/APT
Animal Part Tracker
lbgbox/BiaPy
Open source Python library for building bioimage analysis pipelines
lbgbox/cellpose
a generalist algorithm for cellular segmentation
lbgbox/Data-Science-For-Beginners
10 Weeks, 20 Lessons, Data Science for All!
lbgbox/decoupler-py
Python package to infer biological activities from omics data using a collection of methods.
lbgbox/fq-segmentation
Wrapper code for segmentation of cells and nuclei with Cellpose.
lbgbox/Mask_RCNN
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
lbgbox/ML-YouTube-Courses
📺 A place to discover the latest machine learning courses on YouTube.
lbgbox/napari-chatgpt
A napari plugin to process and analyse images with chatGPT!
lbgbox/Online_R_learning
Online R learning for applied statistics
lbgbox/Patch-GCN
Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks - MICCAI 2021
lbgbox/python-bioimage-analysis-tutorial
The new and improved 2018 version of the EMBL Python BioImage Analysis Tutorial. Now finally in python 3!
lbgbox/python_biologist
Python Programming for Biologists
lbgbox/qupath-extension-cellpose
an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.
lbgbox/RNAlysis
RNA sequencing analysis software
lbgbox/RS-FISH
Tool for precise, interactive, fast and scalable FISH spot detection
lbgbox/scientific-visualization-book
An open access book on scientific visualization using python and matplotlib
lbgbox/scikit-learn
scikit-learn: machine learning in Python
lbgbox/scRNAseq_analysis_vignette
Tutorial for scRNA-seq data analysis beginners using R
lbgbox/single-cell-best-practices
https://www.sc-best-practices.org
lbgbox/single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
lbgbox/sitk-ibex
Aligning images acquired with the IBEX microscopy imaging technique
lbgbox/spark
Apache Spark - A unified analytics engine for large-scale data processing
lbgbox/spatial-transcriptomics-pipeline
lbgbox/stereopy
A toolkit of spatial transcriptomic analysis.
lbgbox/useqfish_analysis
lbgbox/useqfish_probedesign
lbgbox/utag
lbgbox/xDbit_toolbox
Analysis pipeline for multiplexed Deterministic Barcoding in Tissue (xDbit)