198 Open source projects that are alternatives of or similar to squidpy

CellRank for directed single-cell fate mapping

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Wasserstein Generative Adversarial Network for analysing scRNAseq data

Plant Disease Identification Using Convulutional Neural Network

3D Slicer Module for connecting to model repository and use models for image analysis.

A Geometry library for Elixir that calculates spatial relationships between two geometries

A Bayesian model for compositional single-cell data analysis

Remote Sensing and GIS Software Library; python module tools for processing spatial data.

Proof of concept developer code and samples to help be successful with all ArcGIS developer products (Python, NET, JavaScript, Android…). The repository is designed to be an exchange for sharing coding conventions and wisdom to developers at all skill levels.

A curated set of lightweight but powerful tools for on-the-fly image processing and raster analysis in ArcGIS.

All-in-one analysis pipeline

A spatial aware implementation of elliptical Fourier analysis

<<------ Use SnapATAC!!

This repository explores the variety of techniques commonly used to analyze and interpret images. It also describes challenging real-world applications where vision is being successfully used, both for specialized applications such as medical imaging, and for fun, consumer-level tasks such as image editing and stitching, which students can apply…

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

R package for computing spatial position models

A collection of 50+ trajectory inference methods within a common interface 📥📤

R Package for accessing and plotting Google Maps

A R framework for pipeline benchmarking, with application to single-cell RNAseq

A Python software library with a variety of functions for (optical) microscopy image restoration, reconstruction and analysis.

Long list of geospatial tools and resources

Spatial Optimization

Development version of 'spatstat' package ..............................

Powerful, efficient particle trajectory analysis in scientific Python.

GUI for Image processing with Matlab

Learning cell communication from spatial graphs of cells

No description or website provided.

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

Reverse image search tool (SauceNao, ImgOps, trace.moe, and more)

bring sf to spark in production

Project Documentation, Best Practices & Procedures for Spatial Analysis and Mapping Projects

I/O operations for OME-TIFF files in Julia

Deep Learning based cell composition analysis with Scaden.

GPstuff - Gaussian process models for Bayesian analysis

👁️ An authorial set of fundamental Python recipes on Computer Vision and Digital Image Processing.

Kernel Logistic Regression on Focal Mean Embeddings

Library that helps to implement the QuadTree in android, by using splitting images

A pure Nim k-d tree implementation for efficient spatial querying of point data

Collection of mathematical morphology methods and plugins for ImageJ

Raster-based Spatial Analysis for Python

😎Awesome GIS is a collection of geospatial related sources, including cartographic tools, geoanalysis tools, developer tools, data, conference & communities, news, massive open online course, some amazing map sites, and more.

A tool for the spatial analysis of diversity

OSM in memory

ggimg: Graphics Layers for Plotting Image Data with ggplot2

Tidy Geospatial Networks in R

R package to visualize gene expression data based on weighted kernel density estimation

This book serves as an introduction to a whole new way of thinking systematically about geographic data, using geographical analysis and computation to unlock new insights hidden within data.

A unified framework for example-based texture synthesis, developed alongside my master's thesis.

depthmapX is a multi-platform Spatial Network Analysis Software

Interactive Image similarity and Visual Search and Retrieval application

peartree: A library for converting transit data into a directed graph for sketch network analysis.

Toolkit for the generation and analysis of volume eletron microscopy based synaptic connectomes of brain tissue.

Discrete Global Grids for R: Spatial Analysis Done Right

(Latest semester at https://github.com/kmader/Quantitative-Big-Imaging-2019) The material for the Quantitative Big Imaging course at ETHZ for the Spring Semester 2018

Cython bindings for fpzip, a floating point image compression algorithm.

Cloud-based single-cell copy-number variation analysis tool

Find the type or size of an image

No description or website provided.