Application Notes

Using the 3D Cell Explorer-fluo for fluorescence and holotomographic imaging

Time lapse imaging of mouse embryonic stem cells (mESCs) that have been genetically modified to express the fluorescence ubiquitination cell cycle indicator (FUCCI)

  • Learn how to use the 3D Cell Explorer-fluo to record movies that require both fluorescence and 3D refractive index imaging
  • Learn how to analyze the resulting time lapse experiment

Growing and Filming Stem Cells with the 3D Cell Explorer

Performing long-time imaging (up to weeks) of mammalian stem cells, at high spatio-temporal resolution and in 3D

  • Learn how to record unique stem cell movies and export them from the 3D Cell Explorer’s software STEVE
  • Learn how to maintain perfect humidity and CO2 and control temperature .

Visualizing three-dimensional data produced by the 3D Cell Explorer

Visualizing tomographic data in an efficient way is essential for designing further 3D image analysis

  • Export properly your data produced with the 3D Cell Explorer
  • Learn how to prepare your data
  • Learn how to visualize it in optimal ways

3D object detection and segmentation inside an RI map

Using a simple example, a 3D segmentation of HeLa cells nuclei, you will:

  • Learn how to properly segment the nuclei of mammalian cells present in a 3D refractive index map using FIJI
  • Acquire computational tools and knowledge to analyze your images

Quantitative Analysis of 3D Refractive Index Maps

Using two examples i) HeLa cell nuclei and ii) a time series of mouse embryonic stem cell images, you will:

  • Learn how to obtain a set of numerical features that will describe your objects of interest once they have been segmented
  • Learn how to extract a large panel of features from an object as well as simple visualization cases, more advanced 3D object segmentation and feature plotting with a focus on how to calculate dry mass out of refractive index values.

Best Experimental Practices for Live Cell Imaging with the 3D Cell Explorer


  • Learn how to properly set up Nanolive’s top stage incubator such that mammalian cells can be imaged over a long period of time (up to weeks)
  • Learn the key steps for optimal humidity, CO2 and temperature control as well as correct imaging regime