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. 2019 Nov 26;9:17613. doi: 10.1038/s41598-019-54038-9

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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An introduction to the Spa-RQ software tool package. (a) Schematic overview of Spa-RQ, which includes software for image registration (Spa-R) and spatial quantification (Spa-Q). (b) Examples of image sets that can be registered by Spa-R. (c) Upper image panel illustrates the alignment outcomes following Spa-R implementation with different iteration numbers. The registration quality increases with the iteration number, which can be set by users. The lower bar plot shows how the time required for Spa-R registration increases with image size and iteration number. An iteration rate of 100 is recommended to register images on neighbouring 4 µm tissue sections. (d) Overview of the control panel of Spa-Q. A detailed User Manual can be found in the software folder at the official repository. (e) Examples of outputs generated by Spa-Q. For each ROI, a coloured overlay mask is provided in conjunction with an Excel file listing image quantification data. (f) Overview of various image modalities to which Spa-RQ can be applied.