Phase contrast microscopy

OligoMacro Toolset, is an ImageJ macro-toolset aimed at isolating oligodendrocytes from wide-field images, tracking isolated cells, characterizing processes morphology along time, outputting numerical data and plotting them. It takes benefit of ImageJ built-in functions to process images and extract data, and relies on the R software in order to generate graphs.

DeepCell is neural network library for single cell analysis, written in Python and built using TensorFlow and Keras.

DeepCell aids in biological analysis by automatically segmenting and classifying cells in optical microscopy images. This framework consumes raw images and provides uniquely annotated files as an output.

The jupyter session in the read docs are broken, but the one from the GitHub are functional (see usage example )

This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image. It's based on Feature Pyramid Network (FPN) and a ResNet101 backbone.

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