Unraveling cell–cell communication with NicheNet by inferring active ligands from transcriptomics data
Ligand–receptor interactions constitute a fundamental mechanism of cell–cell communication and signaling. NicheNet is a well-established comput…
Tag: Software
A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy
Teravoxel-scale, cellular-resolution images of cleared rodent brains acquired with light-sheet fluorescence microscopy have transformed the way we …
A genome-wide atlas of human cell morphology
A key challenge of the modern genomics era is developing empirical data-driven representations of gene function. Here we present the first unbiased…
Rapid and sensitive protein complex alignment with Foldseek-Multimer
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex structures. Tra…
DeepPrep: an accelerated, scalable and robust pipeline for neuroimaging preprocessing empowered by deep learning
Neuroimaging has entered the era of big data. However, the advancement of preprocessing pipelines falls behind the rapid expansion of data volume, …
Segment Anything for Microscopy
Accurate segmentation of objects in microscopy images remains a bottleneck for many researchers despite the number of tools developed for this purp…
MARBLE: interpretable representations of neural population dynamics using geometric deep learning
The dynamics of neuron populations commonly evolve on low-dimensional manifolds. Thus, we need methods that learn the dynamical processes over neur…
Nellie: automated organelle segmentation, tracking and hierarchical feature extraction in 2D/3D live-cell microscopy
Cellular organelles undergo constant morphological changes and dynamic interactions that are fundamental to cell homeostasis, stress responses and …
Cell2fate infers RNA velocity modules to improve cell fate prediction
RNA velocity exploits the temporal information contained in spliced and unspliced RNA counts to infer transcriptional dynamics. Existing velocity m…