82 dependents
| Package | Description | Downloads/month |
|---|---|---|
| Segmentation tool for biological cells of irregular size and shape in 3D and 2D. | 8K | |
| cell detection in calcium imaging recordings | 5K | |
| spaCR Spatial phenotype analysis of CRISPR–Cas9 screens (spaCR) | 5K | |
| FenestRA: A Napari plugin for LSEC AFM Super-Resolution & Fenestration Analysis. | 3K | |
| Process and analyse live-cell and/or fluorescence imaging data | 3K | |
| Add your description here | 3K | |
| k-atic alignment analysis of fluorescence microscopy | 3K | |
| MicroLive: An Image Processing Toolkit for Quantifying Live-cell Single-Molecule... | 2K | |
| Napari plugin for spatial RNA quantification | 2K | |
| Single molecule tracking in plugin for Napari | 2K | |
| Common code for the Lenstra lab. | 2K | |
| Integrating transcriptional data to decipher the tumor microenvironment with the... | 2K | |
| Minimal app for big fish. | 2K | |
| AI Powered Photoswitchable Screen | 2K | |
| Automatic micro-tubules cut detector. | 2K | |
| Deep-learning enabled quantitative image analysis of cell full lifecycles | 2K | |
| 1K | ||
| SPatial Analysis for CodEX data (SPACEc) | 1K | |
| The feature extraction pipeline lets you extract relevant features from your ima... | 1K | |
| A collection of fractal tasks used for varying ZMB projects. | 1K | |
| Multi-view light sheet microscopy image processing pipeline | 1K | |
| Spatial phenotype analysis of crisp screens (SpaCr) | 1K | |
| Support functions to load imaging data, particularly cell imaging data, into mac... | 957 | |
| FUSE toolkit supports fluorescent cell image alignment and analysis. | 899 | |
| scPortrait is a scalable toolkit to generate single-cell representations from ra... | 870 | |
| 830 | ||
| Standalone Python CLI wrapper around Trackastra for segmentation and tracking on... | 824 | |
| A software library for segmenting and measuring sediment particles in images | 786 | |
| Accelerated CellStitch for 3D labeling of anisotropic image stacks | 774 | |
| Quantifying senescence, the easy way. | 769 | |
| MyoQuant🔬: a tool to automatically quantify pathological features in muscle fibe... | 768 | |
| napari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation t... | 727 | |
| Python interface for automatic calculation of the fusion index in muscle cell cu... | 723 | |
| Bacterial segmentation and analysis platform than can inport/export files in mul... | 705 | |
| Segmentation and counting nuclei of fused cells | 662 | |
| Segmentation of microscopy images and data analysis pipeline with a graphical us... | 595 | |
| Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in... | 588 | |
| Generalized Live Cell Segmentation with DINOv2 Pretraining | 518 | |
| Pipeline for calcium imaging | 518 | |
| A verison of isosegdenoise with strictly defined dependencies for more stable in... | 511 | |
| A generalist model for cell segmentation in image-based spatial transcriptomics | 500 | |
| Numbers and brightness analysis for microscopic image analysis implemented in py... | 427 | |
| A simple plugin to batch segment cells with cellpose | 419 | |
| Pipeline for calcium imaging (fork of the original suite2p) | 411 | |
| Cell/nuclei counter using cellpose models | 395 | |
| Generate consensus 3D cells segmentations by combining 2D cell segmentations fro... | 394 | |
| Interactive and integrated analysis of multiplexed tissue microarrays | 393 | |
| Pipeline for calcium imaging | 376 | |
| Cell identification in high-resolution Spatial Transcriptomics | 349 | |
| Automated pipeline for detecting droplets and inclusions in microscopy images, p... | 322 |
