Image generation

Using a Hamamatsu slide scanner such as the NanoZoomer, you may end up with NDPI files that can't always be directly open in standard image analysis software such as ImageJ. NDPITools is a collection of software that can convert NDPI files to standard TIFF files, possibly cutting them into smaller JPEG or TIFF pieces that will better fit into your computer's memory. It comes with a bundle of plugins for ImageJ which enable the use of the software directly inside ImageJ with point-and-click.

This small plugin demonstrates the use of OpenSlide in java: it  will extract an imageJ roi drawn from the thumbnail of the whole slide image, or the full image at the desired resolution from an hammatsu NDPI file. Note that z stack are not supported by openslide (neitheir ndpiS).

VascuSynth is an ITK-based synthetic image generator. It synthesizes volumetric images of vascular trees and generates a .gxl file of the ground-truth tree structure. VascuSynth receives a number of .txt configuration files and is capable of generating both ground truth ('ideal') images and images with added noise. The user is capable of choosing from a set simple noise additions and artefacts.

Software for computing single molecule localization accuracies and resolution measures

The FandPLimitTool is a GUI based software module that allows users to calculate the limits to the accuracy with which parameters can be estimated from single molecule imaging data. The software supports calculation of limits for the 2D/3D location estimation problem and the 2D/3D distance-estimation/resolution problem. The location estimation problem is concerned with the task of determining the position of a single molecule and the distance-estimation/resolution problem is concerned with the task of determining the distance of separation between two single molecules. The user can calculate limits for a variety of imaging scenarios.

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