Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: The image shown in Fig. 1a (fluorescent Nissl counterstain shown in gray), with (b) and without (a) semitransparent overlay of 147 distinct anatomic regions automatically annotated by NeuroInfo (10 of these 147 regions are annotated in this example). Details are provided in the main text. For abbreviations, see list. The scale bar in (b) represents 2 mm in (a, b).

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques:

Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: The graphical user interface of NeuroInfo. The navigation menu (e) displays a sample image in the coronal plane, with barrel cortex structures selected in yellow and annotations in teal (d, ontology; f, g, reference space). (a, b, h): control toolboxes and viewers.

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques: Control

Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: The NeuroInfo Atlas Calibration Tool and anatomic orientation selection interface. (a) atlas and 2D section image specification; (b) anatomic sectioned plane selection; (c) sectioned direction selection (coronal); (d) section image orientation selection (coronal).

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques: Selection

Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: Results of automatically registering 30 GENSAT section images (gray bars) and 30 CHDI section images (open bars) investigated in the present study with the 3D reference image of the CCF v3, using NeuroInfo. The panels show Tukey boxplots of (a) the scaling factors in X and Y, (b) the values obtained by calculating the Mattes mutual information metric (MMIM), and (c) the processing time, in seconds. Statistically significant differences between the groups are indicated in panels a and b (*; p < 0.01; ***, p < 0.001).

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques:

Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: (a) Plates of 2D view of the CCF v3 showing those regions (marked by asterisks and arrows) that were investigated during the validation experiments. The colors of the frames match the colors of the bars in (b-h). (b-h) Results of the validation experiments, comparing manual delineations (Dms) performed by neuroanatomy experts (ground truth) with automatic delineations (Das) performed by NeuroInfo of the regions shown in (a) on 15 experimental section images of mouse brains. (b,c,e-h) Tukey boxplots of (b) the Dice coefficient, (c) the distance between the centroids of Da and Dm, (e) the difference between the areas of Da and Dm, (f) the percentage of area-Dm that was covered by area-Da (TP), (g) the amount of area-Da outside area-Dm expressed as a percentage of area-Dm (FP), and (h) the absolute area of Dm. (d) Relative number of Das in which the centroid of Da was found within both Da and Dm. Green, yellow and red bars indicate those regions for which the Dice coefficient was found to be >0.7, 0.5–0.7, <0.5, respectively. For abbreviations, see list.

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques: Biomarker Discovery

Journal: The Journal of comparative neurology

Article Title: Automatic navigation system for the mouse brain

doi: 10.1002/cne.24635

Figure Lengend Snippet: Results of the validation experiments, comparing manual delineations (Dms) performed by neuroanatomy experts (ground truth) with automatic delineations (Das) performed by NeuroInfo of the regions shown in Figure 8a on nine experimental section images of mouse brains from the GENSAT project (panels on the left) and on six experimental section images of mouse brains provided by the CHDI foundation (panels on the right). The panels show Tukey boxplots of (a, b) the Dice coefficient, (c, d) the distance between the centroids of Da and Dm, (g, h) the difference between the areas of Da and Dm, (i, j) the percentage of area-Dm that was covered by area-Da (TP), (k, l) the amount of area-Da outside area-Dm expressed as a percentage of area-Dm (FP), and (m, n) the absolute area of Dm. If for a certain region only two values were available, the Tukey boxplot was replaced by a scattered dot plot of the same color with a line at the mean. (e, f) Relative number of Das in which the centroid of Da was found within both Da and Dm. Green, yellow, and red bars indicate those regions for which the Dice coefficient was found to be >0.7, 0.5–0.7, <0.5, respectively. For abbreviations, see list.

Article Snippet: To overcome the challenges of subjective judgments in atlas referencing, we developed a novel mouse brain navigation system (NeuroInfo) that 1) automatically registers images of experimental mouse brain sections with a 3D digital mouse brain atlas that is essentially based on the third version of the Allen Mouse Brain Common Coordinate Framework (CCF v3) ( Allen Institute for Brain Science, 2017 ); 2) retrieves graphical region delineations and annotations from this 3D digital mouse brain atlas; and 3) superimposes this information onto the experimental section image on a computer screen.

Techniques: Biomarker Discovery