Analysis tools and extensions developed at MRI. You can find the complete list of publicly available tools we developed in our github. Please contact us if you have an unsolved image analysis problem. We can either point you to already existing solutions of develop a custom tool for you.

3D Nuclei Clustering Tool

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 Tools

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

Arabidopsis Seedlings Tool

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