TABLE I.

Description of the acquisition and preparation protocols for the multimodal radiology and pathology datasets used for evaluating our analytic framework. The 3D reconstruction of the histology was performed at 0.5x, while the in vivo MRI was resampled to have consistent, close to isotropic voxels sizes of 250 μm³ for feature analysis. The lungs of two Sftpd^−/− mice and one WT mouse were fixed, carefully sliced, and had H&E staining. These histology images were utilized to assess the accuracy of the 3D histology reconstruction approach and the quality of the histology-MRI fusion. The remaining four WT mice were only used for the validation of the textural analysis module. Since the latter four mice are control animals without an inflammation phenotype, no mapping of histology onto the imaging is required and hence was not performed.

Mouse	Count	Modality	Sequence	Resolution (μm3)	Voxels	Annotations
	2	In vivo MRI	T1 GRE	M × M × 500	256 × 256 × N	Lung, blood
				M ∈ {156, 234}	N ∈ {32, 34}	vessels
				M × M × 500	M × M × N	Lung, airways
Sftpd−/−	2	Ex vivo MRI	T1 GRE	M ∈ {125, 156}	M ∈ {256, 512}
					N ∈ {20, 34}
					M × M × N	Lung, airways
	2	Histology		0.75 × 0.75 × 110	M ∈ {5000, 15 000}	Blood vessels
					N ∈ {62, 74}	Inflammation
	1	In vivo MRI	T1 GRE	234 × 234 × 500	256 × 256 × 32	Lung
	1	Ex vivo MRI	T1 GRE	156 × 156 × 500	256 × 256 × 34	Lung, airways
WT	1	Histology		0.75 × 0.75 × 110	M × M × 79	Lung, airways
					M ∈ {5000, 15 000}	Blood vessels
				M × M × N	M × M × N	Lung
	4	In vivo MRI	T1 GRE	M ∈ {156, 500}	M ∈ {128, 256}
				N ∈ {200, 500}	N ∈ {30, 128}