Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2019 Dec 3;10:5504. doi: 10.1038/s41467-019-13374-0

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 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/.

PMC Copyright notice

Fig. 2 — Validation highlighting MIRACL’s registration and segmentation accuracy. a High fidelity of CLARITY registration to the Allen Regional Atlas (ARA). Left: Coronal view of an ARA Nissl histology slice. Center: CLARITY auto-fluorescence channel of a representative stroke mouse registered to the ARA. Right: The same auto-fluorescence channel with overlaid label outlines (R–L: right–left, S-I: superior–inferior). b Axial and coronal views of a Thy1 yellow fluorescence protein (YFP) imaging volume (green) registered to the ARA template (grayscale) and an axial view of another registered CLARITY dataset with (right) and without (left) ARA labels. c Coronal views of three Allen-registered in vivo MR images (a control mouse, a striatal stroke mouse, and a cortico-striatal stroke, respectively). All mice in this study were scanned 24 h after stroke. d Low root mean squared error (RMSE) between transformed manually placed landmarks on the native MRI and CLARITY imaging volumes and ARA manually placed landmarks. Center line of box plot represents the median, bounds represent the first and third quantiles, and whiskers represent the lowest and highest datum within 1.5× the interquartile range of the lower and upper quantiles. e Segmentation results for nuclei using propidium iodide (PI) stain. Coronal view of a PI stroke brain and its corresponding segmentation image (scale bar: 400 µm). Inset (right) shows a zoom-in view on cortex ipsilateral to the stroke with individually segmented cells shown in random colors overlaid on the original PI image (scale bar: 100 µm). f Segmentation results for layer-specific neurons using Thy1-YFP (YFP). Coronal view of a Thy1-YFP stroke brain and its segmentation image (scale bar: 400 µm). Insets (right) show zoom-in views on the cortex contralateral to the stroke (orange box) and cortex ipsilateral to the stroke (blue box) (scale bars: 50 µm). g Zoom-in on YFP results with segmentation overlaid on raw images, and 3D rendering of YFP raw and segmented neurons. h 3D rendering of an original YFP volume with a 5-µm isotropic resolution (left) and examples of voxelized segmentation results (where the segmentation images are summarized at lower resolutions in the Allen space) at 25 µm in two- and three-dimensions (scale bar: 600 µm).