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Cellpose-SAM: cell and nucleus segmentation with superhuman generalization. It can be optimized for your own data, applied in 3D, works on images with shot noise, (an)isotropic blur, undersampling, contrast inversions, regardless of channel order and object sizes.

is a scalable toolkit for RNA velocity analysis in single cells.

is the scverse toolkit for scalable analysis and visualization of spatial molecular data. It builds on scanpy and anndata, providing streamlined APIs for feature extraction, spatial statistics, and interactive exploration of tissue sections together with microscopy images.

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

CellRank is a modular framework to study cellular dynamics based on Markov state modeling of multi-view single-cell data.

CellRank scales to large cell numbers, is fully compatible with the scverse ecosystem, and easy to use. In the backend, it is powered by pyGPCCA (Reuter et al. (2018)).

an easy-to-use Notebook based environment for fast and convenient protein structure predictions.

(single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.

a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

kb-python is a python package for processing single-cell RNA-sequencing. It wraps the kallisto | bustools single-cell RNA-seq command line tools in order to unify multiple processing workflows.