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. Author manuscript; available in PMC: 2019 Nov 6.
Published in final edited form as: Anal Chem. 2018 Oct 16;90(21):12404–12413. doi: 10.1021/acs.analchem.8b02885

Figure 2. Full workflow for registration-driven histology-directed experiments and data analysis strategies.

Figure 2.

A. First, intra-section registration is performed between H&Eserial and AFserial. After intra-section registration, inter-section registration is performed between AFserial & AFIMS. The developed inter-section transformation is then used to transform H&Eserial, thus projecting H&Eserial onto AFIMS. B. With H&Eserial projected onto the section destined for IMS (AFIMS), annotations can be made to the H&E for IMS acquisition. Additionally, the AF provides morphological information that may sometimes be used to verify annotations by overlay of AFIMS and the registered H&Eserial. C. Data is acquired from the section only in the annotated areas. D. After IMS acquisition, the AFIMS section can be stained to compare inter-section H&Es directly. H&Eserial = H&E staining image from the annotation serial section. AFserial = AF image from the annotation serial section. AFIMS = AF image from section destined for IMS. H&EPost-IMS = H&E staining image from the section where IMS was performed, stained after IMS data acquisition.