Universiteit Leiden

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Cell Observatory

OMERO

From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 150 image file formats supported, including all major microscope formats.

Why OMERO

The Cell Observatory within the Faculty of Science at Leiden University contributes to scientific excellence in the life sciences through innovative state-of-the-art imaging technologies. Several institutes contribute to these Advanced Optical Microscopy (AOM) techniques and data analysis workflows. National  and  international  bio-imaging  communities  have  taken  on  the  challenge  of  structured  image  data-management following the FAIR (Findable Accessible Interoperable Reusable) principles. A major challenge for a local infrastructure is therefore the harmonisation of solutions and best practices, standardising the collection of rich metadata and providing a centralized archiving solution for researchers. In all cases, the links between data and  data  analysis  tools  need  improvements,  and  more  support  for  data  stewardship  is  required  throughout  the data life cycle. The data management and image analysis processes have common requirements across all imaging modalities, although different techniques give rise to specific problems and must all be addressed in a common data management and analysis framework. 

Leiden  University  was  one  of  the  first  in  the  Netherlands  to  successfully adopt the  OMERO  database. A centralized OMERO database  will  facilitate  preserving  and  archiving  raw  data,  collaboration  on  data  analysis workflows, and FAIR data management. To advance in archiving, processing and sharing of bio-imaging data, the first Faculty wide OMERO instance was set up as a pilot. This  pilot was  made available  to multiple  researchers who worked with a selection of 4 microscopes from different suppliers. During the course of the pilot (6 months), the OMERO instance has been evaluated. Since september 2020 the pilot has gone live and all researchers can and should upload their microscopic data into OMERO.  

Acccess to OMERO 

Everyone at Leiden University can access OMERO after registration for access (Including bachelor and Master students), for registration contact anyone from the OMERO team. All data can be accessed via the omero webbrowser of after installing the omero insight client. The latter is especially useful when downloading large datasets. All communication about OMERO is done via Teams

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