Imaging Informatics and the Human Brain Project: the Role of Structure, Review

(no abstract

Automatic Recognition of Light Microscope Pollen Images

This paper is a progress report on a project aimed at the realization of a low-cost, automatic, trainable system "AutoStage" for recognition and counting of pollen. Previous work on image feature selection and classification has been extended by design and integration of an XY stage to allow slides to be scanned, an auto focus system, and segmentation software. The results of a series of classification tests are reported, and verified by comparison with classification performance by expert palynologists. A number of technical issues are addressed, including pollen slide preparation and slide sampling protocols

Recursive Training of 2D-3D Convolutional Networks for Neuronal Boundary Detection

Efforts to automate the reconstruction of neural circuits from 3D electron microscopic (EM) brain images are critical for the field of connectomics. An important computation for reconstruction is the detection of neuronal boundaries. Images acquired by serial section EM, a leading 3D EM technique, are highly anisotropic, with inferior quality along the third dimension. For such images, the 2D max-pooling convolutional network has set the standard for performance at boundary detection. Here we achieve a substantial gain in accuracy through three innovations. Following the trend towards deeper networks for object recognition, we use a much deeper network than previously employed for boundary detection. Second, we incorporate 3D as well as 2D filters, to enable computations that use 3D context. Finally, we adopt a recursively trained architecture in which a first network generates a preliminary boundary map that is provided as input along with the original image to a second network that generates a final boundary map. Backpropagation training is accelerated by ZNN, a new implementation of 3D convolutional networks that uses multicore CPU parallelism for speed. Our hybrid 2D-3D architecture could be more generally applicable to other types of anisotropic 3D images, including video, and our recursive framework for any image labeling problem

Cerebral atrophy in mild cognitive impairment and Alzheimer disease: rates and acceleration.

OBJECTIVE: To quantify the regional and global cerebral atrophy rates and assess acceleration rates in healthy controls, subjects with mild cognitive impairment (MCI), and subjects with mild Alzheimer disease (AD). METHODS: Using 0-, 6-, 12-, 18-, 24-, and 36-month MRI scans of controls and subjects with MCI and AD from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we calculated volume change of whole brain, hippocampus, and ventricles between all pairs of scans using the boundary shift integral. RESULTS: We found no evidence of acceleration in whole-brain atrophy rates in any group. There was evidence that hippocampal atrophy rates in MCI subjects accelerate by 0.22%/year2 on average (p = 0.037). There was evidence of acceleration in rates of ventricular enlargement in subjects with MCI (p = 0.001) and AD (p < 0.001), with rates estimated to increase by 0.27 mL/year2 (95% confidence interval 0.12, 0.43) and 0.88 mL/year2 (95% confidence interval 0.47, 1.29), respectively. A post hoc analysis suggested that the acceleration of hippocampal loss in MCI subjects was mainly driven by the MCI subjects that were observed to progress to clinical AD within 3 years of baseline, with this group showing hippocampal atrophy rate acceleration of 0.50%/year2 (p = 0.003). CONCLUSIONS: The small acceleration rates suggest a long period of transition to the pathologic losses seen in clinical AD. The acceleration in hippocampal atrophy rates in MCI subjects in the ADNI seems to be driven by those MCI subjects who concurrently progressed to a clinical diagnosis of AD

Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann’s area 32 and area 21

Published in final edited form as: Brain Struct Funct. 2019 January ; 224(1): 351–362. doi:10.1007/s00429-018-1777-z.Optical coherence tomography is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles. Optical coherence microscopy (OCM) is higher resolution (i.e., 1.25 µm) and is capable of detecting neurons. In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II. In the current method-oriented study, we aimed to determine the colocalization success rate between OCM and Nissl in other brain cortical areas with different laminar arrangements and cell packing density. We focused on two additional cortical areas: medial prefrontal, pre-genual Brodmann area (BA) 32 and lateral temporal BA 21. We present the data as colocalization matrices and as quantitative percentages. The overall average colocalization in OCM compared to Nissl was 67% for BA 32 (47% for Nissl colocalization) and 60% for BA 21 (52% for Nissl colocalization), but with a large variability across cases and layers. One source of variability and confounds could be ascribed to an obscuring effect from large and dense intracortical fiber bundles. Other technical challenges, including obstacles inherent to human brain tissue, are discussed. Despite limitations, OCM is a promising semi-high throughput tool for demonstrating detail at the neuronal level, and, with further development, has distinct potential for the automatic acquisition of large databases as are required for the human brain.Accepted manuscrip