Overview of Image Data Management Platforms for Microscopy Data
Microscopy images are a common type of data across research domains. Modern microscopy is collection of many different imaging techniques with various complexities. Often, microscopy data has a large file size (e.g., data from whole-slide scannners, light sheet microscopes, or high-content imaging systems). In addition, image processing and analysis workflows are either intrinsic steps of image generation, or they are regularly applied on images to obtain quantitative and qualitative information out of pixel intensity values. Given the various microscopy modalities and the large number of vendors for microscopy equipment, at present, microscopy data is heterogenous with respect to its file formats and metadata models. To enable full access to all image information, proprietary software is often required.
For researchers, the organization of raw data, and a good strategy to document the full provenance throughout a data life cycle is an important aspect of good scientific practice. Large file sizes and proprietary formats make data handling demanding. In particular, when data must be shared with other researchers in a collaborative setting, keeping track of when who did what to the data, how data was transfered, and if all steps are properly audited is a time-consuming challenge for many experimentalists.
To ease image data handling, several software were produced to help manage and/or analyse bioimaging data with different degrees of specialization. Using a suitable data management platform helps to organize, preview, annotate, and otherwise act on image data in a well-structured manner. According to the 2021 NFDI4BIOIMAGE community survey, many researchers acknowledge of the benefits of data management systems, but researchers are undecided about the effort-to-benefit ratio to implement such software (Schmidt & Hanne et al., 2022). Dedicated time and hardware resources are needed to set up a well-working data management platform. Hence, providing image data management as a central service for many researchers together creates synergy.
Here, we provide an overview of some selected open-source software platforms for bioimaging data management. Some of these platforms are available in combination with commercial services, and in addition, many commercial providers offer software suites for data management and analysis. Commercial offers are not included here. Many of the introduced software platforms have shared hallmarks as they:
- are suited for (large) imaging-specific data
- are extensible to work with third-party software
- provide organization and analysis functionalities
- have an open-source code and a maintainer community
- have been successfully used in many research projects
The I3D:bio‘s focus is on OMERO because at the time of project planning, it was the best established among applicants, and it was generally declared the most well-known among (German) bioimaging scientists (Schmidt & Hanne et al., 2022). Quick links to the platforms introduced below: