2D

Removal of heterogeneous background from image data of single-molecule localization microscopy, using extreme value-based emitter recovery (EVER).

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EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

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pyTFM is a python package that allows you to analyze force generation and stresses in cells, cell colonies, and confluent cell layers growing on a 2-dimensional surface. This package implements the procedures of Traction Force Microscopy and Monolayer Stress Microscopy. In addition to the standard measures for stress and force generation, it also includes the line tension, a measure for the force transfer exclusively across cell-cell boundaries. pyTFM includes an addon for the image annotation tool clickpoints allowing you to quickly analyze and vizualize large datasets.

AnnotatorJ is a Fiji Plugin to ease annotation of images, particulrly useful for Deep Learning or to validate an alogorithm. Interestingly, it allows annotation for instance segmentation, semantic segmentation, or bounding box annotations. It includes toolssuch as active contours to ease these annotations.

The tool exports rectangular regions, defined with the NDP.view 2 software (hammatsu) from the highest resolution version of the ndpi-images and saves them as tif-files.

Click the button and select the input folder. The input folder must contain pairs of ndpi and ndpa files. The regions will be exported to a subfolder of the input folder names zones.

This Fiji plugin is a python script for CLEM registration using deep learning, but it could be applied in principle to other modalities. The pretrained model was learned on chromatin SEM images and fluorescent staining, but a script is also provided to train an new model, based on CSBDeep. The registration is then performed as a feature based registration, using register virtual stack plugin (which extract features and then perform RANSAc. Editing the script in python gives access to more option (such as the transformation model to be used, similarity by default. Images need to be prepared such that they contain only one channel, but channel of ineterst (to be transformed with the same transformation) can be given as input, and Transform Virtual Stack plugin can be used as well.