Fluorescence microscopy

Rigid registration of time series in 3D. A video tutorial is available (be careful of sounds, the video automatically starts!): [Sample Drift Correction Following 4D Confocal Time-lapse Imaging](http://www.jove.com/video/51086/sample-drift-correction-following-4d-co…)

Normalize the orientation of the images of the Zebrafish embryos.

In the documentation webpage, the aim of the workflow is to normalize the orientation of the images of the Zebrafish embryos, find the point of injection of tumor cells and measure the distribution of Cy3 stained tumor foci.

ImageJ macro implementation of the Workflow described in Ghotra et al (2012). Note that currently only the angle and orientation normalization is implemented in this version.

Sample images are linked in the documentation webpage. 

A clear tutorial on how to write a MATLAB script to segment clustered cells.

The full script is downloadable near the bottom of the article. 

A workflow template to analyze subcellular structures in fluorescence 2D/3D microscopy images based on a Fiji plugin **Squassh** is described in Rizek et al (2014).

The workflow employs detecting, segmenting, and quantifying subcellular structures. For segmentation, it accounts for the microscope optics and for uneven image background. Further analyses include both colocalization and shape analyses. However, it does not work directly for time-lapse data. A brief summary note can be found here.

CellDetector can detect cells (or other objects) in microscopy images such as histopathology, fluorescence, phase contrast, bright field, etc. It uses a machine learning-based method where a cell model is learned from simple dot annotations on a few images for training and predict on test sets. The installation requires some efforts but the instruction is well explained. Training parameters should be tuned for different datasets, but the default settings could be a good starting point.