The Cell Observatory houses cutting-edge bio imaging technology and other facilities, aimed at visualizing the dynamic structures of life - from molecule to cell. It is located in the LMUY building of Leiden University. For researchers requiring access to its infrastructure, the Cell Observatory includes wet labs, office space and a seminar room equipped for 3D visualization. Informal interactions are encouraged in its science lounge.

The Cell Observatory is a shared facility of the Institutes of the Leiden Faculty of Sciences. It is multi-disciplinary and accommodates small research groups, each under the leadership of an independent tenured or tenure-track scientist of international standing. Each of these research groups is responsible for one or more facilities of the Cell Observatory.  The organization of research groups within the Cell Observatory is non-hierarchical and encourages bottom-up initiatives. A lively environment with new opportunities for excellent, enterprising young scientists is stimulated by the annual award of a new tenure-track position within the Cell Observatory.

The Cell Observatory welcomes Masters students from all disciplines and provides the natural home of the Life Science & Technology and Bioinformatics tracks of the Leiden Faculty of Sciences Graduate School. The Cell Observatory encourages the formation of Hot Groups, which include scientists from several research groups and which focus on a clear, closed research problem that can be solved within a limited period. Graduate students participate in these Hot Groups as part of their research training. The Cell Observatory hosts practical courses and summer schools.

The Cell Observatory is financed by Leiden University, the Leiden Faculty of Sciences and the Institutes of the Faculty. Participating research groups of the Cell Observatory actively collaborate in attracting external funding for new research projects and infrastructure. Selling excess capacity of the facilities to commercial enterprises provides an additional source for maintaining and improving the facilities.

The Cell Observatory is a centre of knowledge transfer and the creation of intellectual property. It encourages the development of novel bio-science products and technologies that benefit health and facilitates spinning out start-up companies. It provides support for existing (local) companies by allowing them access to its facilities. It has an active outreach program, informing and enthusing the general public through websites, public appearances, popular lectures, demonstrations and yearly open days.