RDM in Bioimage Analysis
An integral aspect of bioimaging is the processing and analysis of acquired images. Image analysis workflows range in complexity from simple processing steps to sophisticated, highly automated workflow configurations. Documentation of image analysis workflows is vital. In many regards, research data management and bioimage analysis are intricately linked to each other.
Here, we provide an overview and point of entry for research data management related to bioimage analysis, specifically, how to use Bioimage analysis software in combination with OMERO.
Perspective: The motivation for proper RDM in image analysis (by Tom Boissonnet)
Data management is made for bioimage analysts How often have you wondered about how to structure your folders, if you should write metadata within a single txt or json file or in one file for each image, how to name your images consistently so that your code will be able to find them? Well all these problems disappear when you adopt a research data management solution like OMERO. Of course, there is one step that one cannot skip, which is data annotation. But this is outweighed by the benefits you will get. Annotating data without overdoing it First off, there are different kinds of annotation. In the case of Key-Value pairs, the topic is certainly vast, and you should [...]
BioImage Analysis and OMERO
Image Analysis and OMERO While OMERO is not an image analysis software itself, OMERO supports to perform image analysis on the images stored on OMERO's file system through programmatic connections with popular image analysis software or through user-friendly graphical user interfaces. That means, for most data, it is not necessary to download a copy of the data from OMERO to a local disk before image analysis can be performed. Rather, image analysis software can retrieve images directly from OMERO, even in batch, alleviating the workload significantly. Image analysis results, including generated regions of interest (ROIs) can be stored back in OMERO keeping analysis outcomes and original images closely linked. Accessing OMERO from image analysis software [...]
Fiji-assisted batch analysis using Tags in OMERO
Fiji-assisted batch analysis using tags in OMERO Let's explore a discrete example! Assumption: We have collected images in OMERO, organized into 6 datasets, with each dataset containing 30 images. The six datasets reflect experiments, each of which contains images from compound-treated biological samples and control samples (solvent only). That means: 10 images show solvent-control-treated only, 10 images show samples treated with compound X, and 10 images show cells treated with compound Y. In this scenario, each image can be accessed through its position in the dataset and its file name, which includes tokenization to indicate the month of acquisition, the internally defined experiment index (here: A), the compound or solvent treatment, [...]
