We develop software tools for preclinical imaging, including image reconstruction, fusion, segmentation, and quantification. Our software is meant to be user-friendly, efficient, and compatible with any small animal imaging device to enable reproducible quantitative analysis of the acquired multimodal image data. Automation is an important topic in our field because manual analysis is often too time-consuming, error-prone, and hardly reproducible.
Software-based automation can make the analysis efficient and reproducible, but the challenge is in making the automation robust enough. Small animal imaging devices provide volumetric image data of anesthetized laboratory mice and rats, and allow non-invasive assessment of pathological and physiological changes. Integrated multimodal devices combine the strengths of multiple modalities, such as Micro-CT and PET.
It is also possible to combine two separate devices. We developed software for the automated fusion of special modalities, such as Micro-CT and FMT. We also provided efficient software for interactive image fusion, and defined a new file format to store the image data, considering aspects from data curation.
Last year, we published an approach for retrospective respiratory gating under high throughput settings. Our protocol resides in a transformation matrix, which is generated using a calibration step that involves visible structures such as fiducial markers. Then, the image fusion can be automated using this transformation matrix, which eliminates the need for markers.
