Light microscopy

Synonyms
Optical microscopy
Optical microscope
Light microscope

BioImage Model Zoo

Collection
Description

BioImage.IO -- a collaborative effort to bring AI models to the bioimaging community. 

  • Integrated with Fiji, ilastik, ImJoy and more
  • Try model instantly with BioEngine
  • Contribute your models via Github

This is a database of pretrained deep Learning models. 

has topic
Digital histology
Electron microscopy
Light microscopy
Fluorescence microscopy
Machine learning
has function
Image classification
Cell segmentation
Image denoising
need a thumbnail

StarDist - ImageJ

Component
Description

This is the ImageJ/Fiji plugin for StarDist, a cell/nuclei detection method for microscopy images with star-convex shape priors ( typically for Dapi like staining of nuclei). The plugin can be used to apply already trained models to new images.

has topic
Light microscopy
Light-sheet microscopy
Fluorescence microscopy
Multi-photon microscopy
Machine learning
has function
Image segmentation
Cell segmentation
Model-based segmentation
Stardist

DragonFly

Collection
Description

Dragonfly is a software platform for the intuitive inspection of multi-scale multi-modality image data. Its user-friendly experience translates into powerful quantitative findings with high-impact visuals, driven by nuanced easy-to-learn controls.

For segmentation: It provides an engine fior machine Learning, Watershed and superpixel methods, support histological data .

It offers a 3D viewer, and python scripting capacities .

It is free for reserach use, but not for commercial usage.

has topic
Digital histology
Electron microscopy
Light microscopy
Multimodal imaging
Machine learning
has function
Image feature detection
Image segmentation
Interactive segmentation
Object feature extraction
Shape features
Visualisation
Image visualisation
Volume rendering
DragonFly

Holovibes

Collection
Description

Holovibes is a free software dedicated to the calculation of holograms in real-time. Input interferogram data can be grabbed from a digital camera or loaded from files recorded beforehand. Massive amounts of data can be handled robustly at high throughput, saved to disk, and visualized in real-time without any risk of frame dropping thanks to the use of several configurable input and output memory buffers.

Main features

Image acquisition from several digital cameras or from data files
Choice of hologram rendering method
Blazing-fast hologram rendering
Real-time computation of spectrograms
Hologram autofocus
Image and video post-processing
High throughput saving to disc of massive datasets
Batch recording and communication with remote instruments via GPIB

Requirements

A PC with at least 8 GB of RAM
Microsoft Windows 7/10 64-bit operating system
A NVidia graphics card (GeForce GTX 700+ series)
NVidia CUDA 9
A supported digital camera, or raw interferogram files

Use case examples

Holographic microscopy
Holographic OCT
Holographic vibrometry
Holographic angiography
Holographic plethysmography

has topic
Microscopy
Light microscopy
Widefield microscopy
Phase contrast microscopy
has function
Generation
Image generation
Image reconstruction
need a thumbnail
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