TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

Abstract

BackgroundFurther advances in modern microscopy are leading to teravoxel-sized tiled 3D images at high resolution, thus increasing the dimension of the stitching problem of at least two orders of magnitude. The existing software solutions do not seem adequate to address the additional requirements arising from these datasets, such as the minimization of memory usage and the need to process just a small portion of data.ResultsWe propose a free and fully automated 3D Stitching tool designed to match the special requirements coming out of teravoxel-sized tiled microscopy images that is able to stitch them in a reasonable time even on workstations with limited resources. The tool was tested on teravoxel-sized whole mouse brain images with micrometer resolution and it was also compared with the state-of-the-art stitching tools on megavoxel-sized publicy available datasets. This comparison confirmed that the solutions we adopted are suited for stitching very large images and also perform well on datasets with different characteristics. Indeed, some of the algorithms embedded in other stitching tools could be easily integrated in our framework if they turned out to be more effective on other classes of images. To this purpose, we designed a software architecture which separates the strategies that use efficiently memory resources from the algorithms which may depend on the characteristics of the acquired images.ConclusionsTeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently retrieved and processed. We provide TeraStitcher both as standalone application and as plugin of the free software Vaa3D.

Label-free near-infrared reflectance microscopy as a complimentary tool for two-photon fluorescence brain imaging

“…The BS signal from axons could be visualized up to 120 µm deep inside the sample. The images were then automatically stitched with the TeraStiticher tool [16]. This large-scale reconstruction shows the presence of regions where large bundles of axons extending over the entire hippocampal slice could be resolved with subcellular resolution.…”

“…The coronal section of hippocampus consisted in 40 × 40 tiles, each composed by 768(x) × 768(y) × 6(z) RGB stack of images, which yielded a data set of approximately 17 GVoxels. Stitching was therefore performed using TeraStitcher [16], a 3D stitching tool specifically designed to deal with very large images acquired with motorized microscopes that provide reliable nominal tile positions. TeraStitcher 1.9.2 was used, which is able to process multi-channel images.…”

Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains

“…To perform this operation, we used the TeraStitcher, 23 a fully automated stitching tool designed to deal with tiled images of virtually unlimited size. TeraStitcher can run on machines with limited resources with a performance essentially determined only by the transfer rate toward secondary storage.…”

BioImage Informatics: The challenge of knowledge extraction from biological images

“…While the first uses the morphology to align the raw data, the second stitches together separately image regions. With regard to this last stage, a recent contribution, named as TeraStitcher stitches teravoxelsized microscopy images in a reasonable time even on workstations with limited resources [30]. The Authors claimed that the general approach of other 3D stitching tools suffers from the large dimensions of such image stacks, being useless in these cases.…”