Microscopy

Smooth 2D Manifold Extraction (SME).

Three-dimensional fluorescence microscopy followed by image processing is routinely used to study biological objects at various scales such as cells and tissue. However, maximum intensity projection, the most broadly used rendering tool, extracts a discontinuous layer of voxels, obliviously creating important artifacts and possibly misleading interpretation. Here we propose smooth manifold extraction, an algorithm that produces a continuous focused 2D extraction from a 3D volume, hence preserving local spatial relationships. We demonstrate the usefulness of our approach by applying it to various biological applications using confocal and wide-field microscopy 3D image stacks. We provide a parameter-free ImageJ/Fiji plugin that allows 2D visualization and interpretation of 3D image stacks with maximum accuracy.

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

DeconvolutionLab2 includes a friendly user interface to run the following deconvolution algortihms: Regularized Inverse Filter, Tikhonov Inverse Filter, Naive Inverse Filter, Richardson-Lucy, Richardson-Lucy Total Variation, Landweber (Linear Least Squares), Non-negative Least Squares, Bounded-Variable Least Squares, Van Cittert, Tikhonov-Miller, Iterative Constraint Tikhonov-Miller, FISTA, ISTA.

The backbone of our software architecture is a library that contains the number-crunching elements of the deconvolution task. It includes the tool for a complete validation pipeline. Inquisitive minds inclined to peruse the code will find it fosters the understanding of deconvolution.

The software FishInspector provides automatic feature detections in images of zebrafish embryos (body size, eye size, pigmentation). It is Matlab-based and provided as a Windows executable (no matlab installation needed).

The recent version requires images of a lateral position. It is important that the position is precise since deviation may confound with feature annotations. Images from any source can be used. However, depending on the image properties parameters may have to be adjusted. Furthermore, images obtained with normal microscope and not using an automated position system with embryos in glass capillaries require conversion using a KNIME workflow (the workflow is available as well). As a result of the analysis the software provides JSON files that contain the coordinates of the features. Coordinates are provided for eye, fish contour, notochord , otoliths, yolk sac, pericard and swimbladder. Furthermore, pigment cells in the notochord area are detected. Additional features can be manually annotated. It is the aim of the software to provide the coordinates, which may then be analysed subsequently to identify and quantify changes in the morphology of zebrafish embryos.

This is a classical workflow for spot detection or blob like structures (vesicules, melanosomes,...)

Step 1 Laplacian of Gaussian to enhance spots . Paraeters= radius, about the average spot radius

Step 2 Detect minima (using Find Maxima with light background option to get minima). Parameter : Tolerance to Noise: to be tested, hard to predict. About the height of the enhanced feautures peaks