Summary:
Researchers in UCLA’s Department of Neurobiology have developed a novel software tool that enhances the capabilities of Imaris Stitcher. The tool enables batch processing and automated execution of multiple image stitching jobs, significantly improving workflow efficiency and reducing hands-on time. This results in readily available, combined, aligned, high-resolution microscopic images with a faster overall turnaround.
Background:
Image stitching has emerged as a solution to the unique need for a complete high-resolution image of microscopic data when the subject exceeds the microscope’s field of view. Individual images are captured with overlap and then aligned and stitched together to limit deformations in the data and produce clearer images for analysis. Imaris Stitcher, developed by Oxford Instruments, is an industry-standard solution for this, providing high-quality microscopic image processing.
While Imaris Stitcher excels at producing high-quality stitched images, processing multiple image volumes sequentially can be time-consuming for researchers. For instance, stitching a single image volume might take several hours, and processing a set of images (e.g., six volumes) can require repeated manual initiation for each volume, extending the total processing time over multiple workdays. This traditional workflow requires significant operator attention for each step. There is a need to streamline this process, particularly for projects involving numerous image volumes, to maximize throughput and minimize manual intervention.
Innovation:
Addressing this workflow challenge, UCLA BRAIN researchers Ian Bowman and Mitchell Rudd developed a specialized software tool that interfaces with Imaris Stitcher to automate the processing of multiple image volumes in a batch sequence.
The key innovation of the tool is its ability to manage and automate the Imaris Stitcher operations for a batch of images. Once the initial alignment parameters are saved for each image volume, the tool uses these parameters as input to run the stitching jobs in a continuous batch process, either in parallel or immediate sequence. This means a task that could take several days of attended work can be completed overnight without supervision. This streamlines the workflow around Imaris Stitcher, enabling high-resolution, precisely aligned image volumes to be available more rapidly while significantly enhancing the productivity and throughput of imaging projects.
Potential Applications:
● 3D image reconstruction
● Biomedical imaging for brain and organs
● Live-cell microscopy
● Medical mapping
● AI automated image analysis
● Digital pathology
Advantages:
● Parallelized workflow automation
● 3-6X image processing throughput
● Optimized interactivity
● Expedited multi-volume processing
● User-focused image alignment
State of Development:
The proposed software has been developed and tested to corroborate its use and advantages coupled with ImarisStitcher.
Reference:
UCLA Case No. 2025-089
Lead Inventor:
Ian Bowman, Department of Neurobiology