lbgbox

Pinned Repositories

AIRLOCALIZE
Software for spot detection
Language:MATLAB1 0 00
bioanalyze-docker-images
Docker Images for Jupyterhub + Bioinformatics
Language:Dockerfile1 0 00
DNAbarcodes
Simple generator of DNA barcodes for sequencing experiments
Language:Python1 0 00
EASI-FISH
Tools and scripts for EASI-FISH image data analysis
Language:Jupyter Notebook1 0 00
elastix
Official elastix repository
Language:C++1 0 00
FISHscale
Spatial analysis of FISH data
Language:Jupyter Notebook1 0 00
metacell
Metacell - Single-cell mRNA Analysis
Language:R1 0 00
postcode
Decoding of image-based spatial transcriptomics
Language:Jupyter Notebook1 0 00
qupath-extension-warpy
ImgLib2 RealTransform brought to QuPath
Language:Java1 1 00
starfish
starfish: unified pipelines for image-based transcriptomics
Language:Python1 0 00

lbgbox's Repositories

lbgbox/DNAbarcodes
Simple generator of DNA barcodes for sequencing experiments
Language:Python1 0 00
lbgbox/elastix
Official elastix repository
Language:C++1 0 00
lbgbox/FISHscale
Spatial analysis of FISH data
Language:Jupyter Notebook1 0 00
lbgbox/metacell
Metacell - Single-cell mRNA Analysis
Language:R1 0 00
lbgbox/qupath-extension-warpy
ImgLib2 RealTransform brought to QuPath
Language:Java1 1 00
lbgbox/starfish
starfish: unified pipelines for image-based transcriptomics
Language:Python1 0 00
lbgbox/2016_bray_natprot
Supporting data files, documentation, and updated tips for the Cell Painting protocol
lbgbox/ashlar
ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
Language:Python0 0
lbgbox/cell2location
Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
Language:Python0 0
lbgbox/cellpose_segmentation
Galaxy tool for for cell and nucleus segmentation using Cellpose
lbgbox/cellxgene-documentation
Documentation for the cellxgene product
lbgbox/CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
Language:Python0 0
lbgbox/connected-components-3d
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.
lbgbox/GutAnalysisToolbox
Semi-automated analysis and characterisation of cells within the gut wall.
Language:ImageJ Macro0 0
lbgbox/ijl-utilities-wrappers
Wrappers for external software calls (Cellpose, Elastix, Ilastix...) and java utilities (object conversions and display)
Language:Java1 0
lbgbox/infercnv
Inferring CNV from Single-Cell RNA-Seq
lbgbox/labkit-ui
Advanced Tool for Labeling And Segmentation
lbgbox/Lenstralab-smFISH
Language:Python
lbgbox/mario-py
MARIO: single-cell proteomic data matching and integration using both shared and distinct features
Language:Jupyter Notebook0 0
lbgbox/mIFTO
Multiplex Immunoflouresence Titration Optimization (mIFTO) R Package
Language:R0 0
lbgbox/MorphoLibJ
Collection of mathematical morphology methods and plugins for ImageJ
Language:Java0 0
lbgbox/multifish
EASI-FISH analysis pipeline for spatial transcriptomics
Language:Nextflow0 0
lbgbox/pysmFISH_auto
Version of the pysmFISH pipeline that run without human in the loop
lbgbox/scg_lib_structs
Collections of library structure and sequence of popular single cell genomic methods
lbgbox/scikit-image
Image processing in Python
lbgbox/scimap
Spatial Single-Cell Analysis Toolkit
Language:Python0 0
lbgbox/scimap_phenotyping
Galaxy tool wrapper for single cell phenotyping analysis using Scimap
lbgbox/SMART-Q
Language:Python
lbgbox/smFISH
1 0
lbgbox/TissueSchematics
Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"