Application Notes


When holotomography meets immuno-oncology

In this application note we will discuss new research possibilities offered by the 3D Cell Explorer for the study of immune system cells, which are extremely sensitive to stress.

  • Learn about new research possibilities to study cell-cell interactions within the immune system with a focus on T-cell interactions with self and non-self cells
  • Learn about unique time-lapse imaging of immune system cells that have been produced with the 3D Cell Explorer
Mitochondria - label-free live cell imaging with Nanolive

Investigating cellular metabolism with the 3D Cell Explorer

In this application note we will discuss new research possibilities offered by the 3D Cell Explorer for the study of organelle biology with a focus on mitochondria and lipid droplets biology in both qualitative and quantitative approaches in perturbed or unperturbed conditions.

  • Learn how to observe the fundamental interplay between mitochondria and lipid droplets
  • Learn how to observe and compare mitochondrial network perturbation 
  • Learn how to track lipid droplets

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