Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR.
Bioinformatics
; 38(19): 4613-4621, 2022 09 30.
Article
em En
| MEDLINE
| ID: mdl-35972352
ABSTRACT
MOTIVATION Stitching microscope images into a mosaic is an essential step in the analysis and visualization of large biological specimens, particularly human and animal tissues. Recent approaches to highly multiplexed imaging generate high-plex data from sequential rounds of lower-plex imaging. These multiplexed imaging methods promise to yield precise molecular single-cell data and information on cellular neighborhoods and tissue architecture. However, attaining mosaic images with single-cell accuracy requires robust image stitching and image registration capabilities that are not met by existing methods. RESULTS:
We describe the development and testing of ASHLAR, a Python tool for coordinated stitching and registration of 103 or more individual multiplexed images to generate accurate whole-slide mosaics. ASHLAR reads image formats from most commercial microscopes and slide scanners, and we show that it performs better than existing open-source and commercial software. ASHLAR outputs standard OME-TIFF images that are ready for analysis by other open-source tools and recently developed image analysis pipelines. AVAILABILITY AND IMPLEMENTATION ASHLAR is written in Python and is available under the MIT license at https//github.com/labsyspharm/ashlar. The newly published data underlying this article are available in Sage Synapse at https//dx.doi.org/10.7303/syn25826362; the availability of other previously published data re-analyzed in this article is described in Supplementary Table S4. An informational website with user guides and test data is available at https//labsyspharm.github.io/ashlar/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Base de dados:
MEDLINE
Assunto principal:
Software
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Neoplasias
Limite:
Animals
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Humans
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article