Automated workflow for parallel Multiview Reconstruction


Automated workflow for performing multiview reconstruction of large multiview, multichannel, multiillumination time-lapse SPIM data on a high performance computing (HPC) cluster or on a single workstation. 

Detection of Molecules - DoM


A collection of components for super resolution image data:

  • Detect Molecules
  • Reconstruct Image
  • Results table
  • Drift correction
  • Chromatic correction


HyphaTracker Workflow

HyphaTracker propose a workflow for time-resolved analysis of conidia germination. Each part of this workflow can also be used independnatly , as a toolbox. It has been tested on bright-field microscopic images of conidial germination. Its purpose is mainly to identify the germlings and to remove crossing hyphae, and measure the dynamics of their growth.


Multiview Reconstruction


The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks. 

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Drift correction using PALMsiever


Two workflows are proposed here:

one based on fiducials, the other one on cross-correlation.

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Manual Frame Drift Registration


An ImageJ macro for correcting frame drift occurred during image acquisition.

It often happens that you have an image sequence that shows problematic drifting of image frame and at the same time you have some landmarks that could be used for correcting the drift. This ImageJ macro allows you to Manually track the landmark using ImageJ Manual Tracking Plugin. Using the coordinates recorded in the Result window, each frame is shifted back so that the landmark stays in a single place.