Reverse Dependencies of cellpose

The following projects have a declared dependency on cellpose:

• aind-large-scale-cellpose — Large-scale prediction with cellpose
• AIPyS — AI Powered Photoswitchable Screen
• Cellamander — A package for combining Cellpose gradients for cell phenotyping
• celldetective — description
• cellmap-models — Repository of model architectures and network weights used for CellMap segmentations.
• CellPatchExtraction — no summary
• cellphe — CellPhe: Toolkit for cell phenotyping from time-lapse videos
• cellpose-counter — Cell/nuclei counter using cellpose models
• cellpose-napari — a generalist algorithm for anatomical segmentation
• confluentfucci — no summary
• cut-detector — Automatic Cut Detector
• efficientbioai — efficientbioai is a python package for efficient deep learning in bioimaging
• element-zstack — DataJoint Element for Volume Segmentation
• faim-wako-searchfirst — no summary
• findmycells — An end-to-end bioimage analysis pipeline with state-of-the-art tools for non-coding experts
• FISH-analysis — FISH image analysis library
• fractal-tasks-core — Core bioimage-analysis library and tasks of the Fractal analytics platform
• fuse-toolkit — FUSE toolkit supports fluorescent cell image alignment and analysis.
• HiTIPS — HiTIPS: High-Throughput Image Processing Software for FISH data analysis
• imagegrains — A software library for segmenting and measuring of sedimentary particles in images
• IMC — A package for processing and analysis of imaging mass cytometry (IMC) data.
• jinxif — A python3-based image analysis package to achieve fully-documented and reproducible visualization and analysis of bio-medical microscopy images. This is a fork from Jennifer Eng`s mplex_image software library.
• koopa — Workflow for analysis of cellular microscopy data.
• microscope-napari — Nanobiosensorics microscopic napari plugin.
• morphodynamics — Cell segmentation and windowing
• mplexable — A python3-based image analysis package to achieve fully-documented and reproducible visualization and analysis of bio-medical microscopy images. This is a fork from Jennifer Eng`s mplex_image software library.
• myoquant — MyoQuant🔬: a tool to automatically quantify pathological features in muscle fiber histology images.
• napari-activelearning — An active learning plugin for fine tuning of deep learning models.
• napari-bacseg — Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
• napari-convpaint — A plugin for segmentation by pixel classification using convolutional feature extraction
• napari-moltrack — A user-friendly SMLM analysis platfrom for napari, which includes single molecule localisation, tracking, and analysis features.
• napari-morphodynamics — Interface to run the morphodynamics package.
• napari-PixSeq — A Napari plugin for extracting time series traces from Single Molecule Localisation Microsocpy (SMLM) data.
• napari-prism — A Python package for the inteRactive and Integrated analySis of Multiplexed tissue microarrays
• napari-serialcellpose — A simple plugin to batch segment cells with cellpose
• napari-steinpose — A plugin to process Imaging Mass Cytometry data with cellpose and steinbock
• neura-library — Utility tools for system neuroscience research, including Open Source Wrapper or Parser
• openst — The computational pipeline for the Open-ST method.
• PartSeg-cellpose — PartSeg plugin to use cellpose,
• prismtoolbox — Toolbox for histopathology image analysis
• pyxelperfect — Collection of python powered image-processing functions
• rpegment — no summary
• rsnaped — Python module for single-molecule image processing.
• scip — Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image
• scip-workflows — no summary
• scSpatial — Package used to analyse spatial transcriptomics data with build in segmentation and information transfer
• slideflow — Deep learning tools for digital histology
• small-fish-gui — Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
• sopa — Spatial-omics pipeline and analysis
• SPACEc — SPatial Analysis for CodEX data (SPACEc)
• spacr — Spatial phenotype analysis of crisp screens (SpaCr)
• spots-in-yeasts — A Napari plugin segmenting yeast cells and fluo spots to extract statistics.
• steinbock — A toolkit for processing multiplexed tissue images
• suite2p — Pipeline for calcium imaging
• suite2p-haisslab — Pipeline for calcium imaging
• tllab-common — Common code for the Lenstra lab.
• viscy — computer vision for image-based phenotyping of single cells
• vollseg — Segmentation tool for biological cells of irregular size and shape in 3D and 2D.
• vpt-plugin-cellpose — Cellpose Plugin for VPT
• vpt-plugin-cellpose2 — Cellpose 2 Plugin for VPT