Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. They clustered with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.
Download and further informations: 3D_Nuclei_Clustering_Tool on github
Adipocytes, are the cells that primarily compose adipose tissue, specialized in storing energy as fat. The tool allows to segment the adipocytes in images from histological sections. Once segmented the size of the cells can me measured and their morphology can be analyzed.
Download and further informations: Adipocytes Tools sur github
The Arabidopsis Seedlings Tool allows to measure the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well.
Download and further informations: Arabidopsis Seedlings Tool on github
The tool calculates the ratio of the intensity in the nuclei and the cytoplasm. It needs two images as input: the cytoplasm channel and the nuclei channel. The nuclei channel is used to segment the nuclei. The measurements are made in the cytoplasm channel after the background intensity has been corrected.
Download and further informations: Intensity Ratio Nuclei Cytoplasm Tool on github
Napari-Bigfish is a plugin for the multi-dimensional image viewer napari. It provides an alternative graphical user interface to parts of the Big-FISH python package. Big-FISH is a python package for the analysis of smFISH images.
The tool can be used to analyze scratch assays. It measures the area of a wound in a cellular tissue on a stack of images representing a time-series.
Download and further informations: Wound Healing Tool on github