3D Cell Culture Assays

Numerous ibidi products are made for 3D applications. Examples of 3D matrices are, collagen type I gels, fibrin gels, MatriGel TM*, or synthetic hydrogels. In 3D assays, cells are brought inside, or on top of, an in vivo-like gel matrix. As with all ibidi μ-Slides, cells are being analyzed using fluorescence microscopy, in most cases.

Cell Culture in 3D


For a very simple culture of cells embedded in a 3D gel matrix, the µ-Slide Angiogenesis and the µ-Slide III 3D Perfusion are recommended. In both products, cells can be cultivated in or on a gel layer. Oxygen, the growth medium, or treatments can be delivered and exchanged via the liquid over the gel layer. In the µ-Slide III 3D Perfusion, this liquid can be renewed permanently with a constant flow that enables cell survival for many weeks.

Find more information on Collagen I gel matrices at:
Application Note 26: Fabrication of Collagen I Gels (PDF)

ibidi Products used for this Application:

Migration and Chemotaxis in 3D


For migration and chemotaxis experiments, cells are cultivated in a 3D matrix with a chemical gradient for chemotaxis. This is a typical application for lymphocytes, neutrophils, and T-cells, but also for slow migrating cells like fibroblasts, tumor cells, and stem cells.

Find more information at:
Applicaton Note 17: Chemotaxis 3D (PDF)
Application Note 23: 3D Chemotaxis Protocol for Non-Adherent Cells in a Gel Matrix (PDF)

ibidi Products used for this Application:

Cell Spheroid or Micro Tumor


When utilizing the well-in-a-well feature of the ibidi µ-Slide Angiogenesis, a cell spheroid (or micro tumor) is cultivated on top of, or embedded in, a 3D matrix for long-term cultivation. With the upper well filled with growth medium, nutrients are provided by means of diffusion.


In our µ-Slide III 3D Perfusion, a spheroid (or micro tumor) can be embedded in a gel matrix, like a Collagen Type I gel. The special channel geometry allows for superfusion with a low flow rate (e.g., utilizing the ibidi Pump System). This setup makes long-term cultivation possible for up to several weeks.

Find more information at:
Application Note 32: Generation of Spheroids (PDF)

ibidi Products used for this Application:

Cells in 3D Matrix Under Interstitial Flow


When applying an interstitial flow, we recommend cultivating cells in a 3D matrix in a channel slide. Interstitial flow in a channel is easily applied by using a soft perfusion with growth medium or reagents.

ibidi Products used for this Application:

Application Notes

AN 26: Collagen I Gel for 3D Cell Culture (PDF)
Fabrication protocols for collagen I gel (bovine and rat tail) with different cell media.

AN 32: Generation of Spheroids (PDF)
Generation of spheroids using the liquid overlay technique.