portugueslab / flammkuchen
Flexible HDF5 saving/loading library forked from deepdish (University of Chicago) and maintained by the Portugues lab
☆16Updated last year
Related projects: ⓘ
- A multi-dimensional spatial image data structure for scientific Python.☆37Updated 2 months ago
- Image registration (alignment) software for large microscopy images☆21Updated 11 months ago
- An automatic deep learning algorithm for spot detection in fluorescence microscopy images.☆16Updated last week
- ☆10Updated 4 months ago
- Tools and scripts for EASI-FISH image data analysis☆17Updated last year
- R package to infer spatial location of neuronal subpopulations within the developing mouse brain by integrating single-cell RNA-seq data …☆17Updated 9 years ago
- Graph-based Decoding for In Situ Sequencing☆10Updated 4 years ago
- A toolkit to quantify cell dynamics in living tissues☆11Updated 5 years ago
- EASI-FISH analysis pipeline for spatial transcriptomics☆32Updated last month
- Python API and Jupyter widget for Vitessce☆37Updated this week
- ☆28Updated 4 months ago
- ☆27Updated last year
- MERlin is an extensible analysis pipeline applied to decoding MERFISH data☆34Updated 3 years ago
- This repository contains the code used for the paper "Molecular Atlas of the Adult Mouse Brain".☆15Updated 3 years ago
- LaTeX template to create a compiled PDF (text+figures) e.g. for bioRxiv.org☆20Updated 8 years ago
- A Python package for single-cell spatial image analysis.☆18Updated last year
- manually align specimens to annotated 3D spaces☆19Updated last year
- Work with trained factor models in Python☆25Updated 7 months ago
- Interactive visualization of spatial omics data☆36Updated this week
- pMoSS (p-value Model using the Sample Size) is a Python code to model the p-value as an n-dependent function using Monte Carlo cross-vali…☆16Updated 6 months ago
- Alignment of spatial genomics data using deep Gaussian processes☆24Updated last year
- Nextflow pipeline encapsulating workflows for analyzing expansion lattice light-sheet microscopy (ExLLSM) imagery☆13Updated 10 months ago
- Light-weight Jupyter notebook tracker.☆34Updated last month
- Powerful and lightweight package to identify tissue compartments in spatial transcriptomics datasets.☆15Updated 2 weeks ago
- Fast reconstruction of spatial networks from bioimages.☆24Updated last month
- A plugin to visualise 3D spatial single cell omics☆21Updated 5 months ago
- Allen Brain Atlas utilities, parsers and data structures☆10Updated 7 years ago
- TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUma…☆20Updated last year
- Library for managing, storage, viewing, and working with spatial transcriptomics data using Imglib2, N5, BigDataViewer and Fiji.☆25Updated last month
- A Python package using Gromov-Wasserstein distance to compare cell shapes☆14Updated last week