ilastik

Fiji/ImageJ — batteries-included distribution of ImageJ2 for scientific bioimage analysis. Batch macro scripting for cell counting, fluorescence quantification, and particle tracking. Bio-Formats supp

2 shared topics • 2 shared operations

Cellpose — generalist deep learning algorithm for cellular and nuclear segmentation in microscopy images. Provides GPU-accelerated 2D and 3D instance segmentation using gradient flow representations,

2 shared topics • 1 shared operation

DeepCell — deep learning library for single-cell analysis of biological images using TensorFlow. Provides pretrained models for cell segmentation including Mesmer (multiplexed tissue imaging), nuclear

2 shared topics • 1 shared operation

QuPath — open-source platform for whole slide image analysis and digital pathology. Provides interactive tools for tissue detection via thresholding, cell detection and positive cell classification (H

2 shared topics • 1 shared operation

ZeroCostDL4Mic is a Google Colab-based platform providing zero-cost deep learning for fluorescence microscopy image analysis. Supports segmentation (U-Net, StarDist, Cellpose), denoising (Noise2Void,

2 shared topics • 1 shared operation