Arivis: Zeiss software solution for image processing and analysis

 The issue: there are different solutions regarding image processing and analysis available, some of them open-sourced, like Fiji/ImageJ, while others are from private companies, like Imaris or Neurolucida, the later case being more specific for analysis of neuroscience images. Some others are directly connected with big microscopy producers, and in this post I am going to talk about the one that Zeiss chose as their partner, Arivis. 

Solution: In the following site, there is the description of an Arivis pipeline that the applications development engineer Dr Kallioupi Arkoudi uses for segmenting and identifying individual neurons. The sample comes from a fixed Thy1-GFP-Mouse brain and the picture was acquired by using a Zeiss LSM 980 laser scanning confocal. The program is modular, in the sense that the user can build his/her own pipeline depending on the type of image or structure they are trying to identify and analyse. From what I understood, there is also an online alternative called Arivis Cloud that somehow fused or stemmed from Zeiss previous analysis software Apeer. 

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