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Description

ND-SAFIR is a software for denoising n-dimentionnal images especially dedicated to microscopy image sequence analysis. It is able to deal with 2D, 3D, 2D+time, 3D+time images have one or more color channel. It is adapted to Gaussian and Poisson-Gaussian noise which are usually encountered in photonic imaging. Several papers describe the detail of the method used in ndsafir to recover noise free images (see references).

It is available either in Metamorph (commercial version), either as command line tool. Source are available on demand.

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Description

Deep learning based image restoration methods have recently been made available to restore images from under-exposed imaging conditions, increase spatio-temporal resolution (CARE) or self-supervised image denoising (Noise2Void). These powerful methods outperform conventional state-of-the-art methods and leverage down-stream analyses significantly such as segmentation and quantification.

To bring these new tools to a broader platform in the image analysis community, we developed a simple Jupyter based graphical user interface for CARE and Noise2Void, which lowers the burden for non-programmers and biologists to access these powerful methods in their daily routine.  CARE-less supports temporal, multi-channel image and volumetric data and many file formats by using the bioformats library. The user is guided through the different computation steps via inline documentation. For standard use cases, the graphical user interface exposes the most relevant parameters such as patch size and number of training iterations, while expert users still have access to advanced parameters such as U-net depth and kernel sizes. In addition, CARE-less provides visual outputs for training convergence and restoration quality. Any project settings can be stored and reused from command line for processing on compute clusters. The generated output files preserve important meta-data such as pixel sizes, axial spacing and time intervals.

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Description

VAST (Volume Annotation and Segmentation Tool) is a utility application for manual annotation of large EM stacks.

General labeling tool, used for a large variety of 3D data sets; electron-microscopic, multi-channel light-microscopic, and Micro-CT data sets as well as videos, and annotating arbitrary structures, regions and locations, depending on the user’s needs.

Description

PSFj is a software tool that automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations. PSFj provides reporting functions to document the momentary performance of a system and it allows for the export of the obtained data, e.g. for image restoration purposes. PSFj is based on ImageJ and JAVA, and runs on Windows, Mac, and Linux PCs as a stand-alone application.

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Description

QuickFit 3 is a data evaluation software for FCS Fluorescence Correlation Spectroscopy and imagingFCS (imFCS) measurements, developed in the group B040 (Prof. Jörg Langowski) at the German Cancer Research Center (DKFZ). Actually QuickFit 3 itself is a project manager and all functionality is added as plugins. A set of tested plugins for FCS, imagingFCS and some microscopy-related image processing tasks is supplied together with the software.

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