Linux

[as of 20180524, the website is temporary not functioning do to web defacement - please check again later] This tutorial will exemplify basic rapidSTORM usage by showing how to convert an Andor SIF acquisition to a super-resoluted image with rapidSTORM.

A deconvolution component applicable to confocal and STED microscopy. The MATLAB function fo this package implements the SGP method for n-dimensional object deblurring with the option of boundary effects removal. Although this is a preliminary version, results seem to be good from their paper (Zanella et al 2013).

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.

This plugin will return on a full 256-grey level image (limitation in this version) or on a ROI several texture features such as described in Haralick publication. Can be run in batch mode.

This Javascript works in ImageJ to measure 3D intensity profile along cylindrical space with variable radius.