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Here, we present Brain Registration and Evaluation for Zebrafish (BREEZE)-mapping, a user-friendly pipeline for the registration and analysis of whole-brain images in larval zebrafish. We describe steps for pre-processing, registration, quantification, and visualization of whole-brain phenotypes in zebrafish mutants of genes associated with neurodevelopmental and neuropsychiatric disorders. By utilizing BioImage Suite Web, an open-source software package originally developed for processing human brain imaging data, we provide a highly accessible whole-brain mapping protocol developed for users with general computational proficiency. For complete details on the use and execution of this protocol, please refer to Weinschutz Mendes et al. (2023). 1 ., Competing Interests: Declaration of interests X.P. is a consultant for the Brain Electrophysiology Laboratory Company. X.P. also consults and has an ownership stake in Veridat., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Removal of the interplane septa and configuration of a typical multislice PET scanner to accept all possible coincidence lines of response leads to a fivefold increase in sensitivity. This can be of value in regional CBF studies using bolus 15O-labeled water injections, allowing the injected dose to be reduced by a factor of 4, while maintaining the same number of noise equivalent counts. Thus, for a given cumulative dose limit, four times as many studies can be performed in a single subject. Data from the three-dimensional Hoffman brain phantom, closely matched to count rates seen in human studies, show that for an identical cumulative dose, the noise in subtraction (stimulus minus baseline) images can be reduced by a factor of 2 using three-dimensional data acquisition, with appropriate fractionation of the dose. This improvement is dependent on axial position due to the sensitivity characteristics of three-dimensional scans; however, there is a significant gain in the signal-to-noise ratio (S/N) in all image planes. Studies performed in a human subject demonstrate how the factor of 2 gain in S/N leads to improved detectability of activation sites in PET subtraction images.

The results of a receiver operator characteristic (ROC) study comparing maximum likelihood estimator (MLE) reconstructions of human FDG PET brain scan data to filtered backprojection reconstructions of the same data are reported. The purpose of the study was to determine whether MLE reconstructions would result in higher detectability of small focal lesions introduced artificially into otherwise normal scan data. One physician assisted in defining the location and intensity of the lesions and five physicians read the final images. Data from 90 datasets were used for the study. Of those, 42 were left in their original "normal" condition and 48 were modified by added lesions. All datasets were reconstructed by the two methods and submitted to the five physicians for evaluation. The results show an increase in the area under the ROC curve from approximately 0.65 for filtered backprojection to approximately 0.71 for the maximum likelihood reconstructions for four of the five observers with good statistical significance.

We have developed a three-dimensional computer simulation of SPECT imaging. We have applied the simulation procedure to the realistic mathematical Hoffman three-dimensional brain model to generate the projection data (in the absence of attenuation, scatter, or noise) of both a parallel-hole and a multidetector SPECT system with point-focusing collimators. The simulated projection data were then reconstructed using standard software. The projection data resulting from the distribution of grey matter alone, or grey and white matter, were simulated. The results of these simulations indicate the existence of significant qualitative and quantitative artifacts in reconstructed human brain images. For example, the reconstructed values for grey matter along a cortical circumferential profile in a transverse slice through the basal ganglia varied by a factor of 2.40 (parallel-hole) and 2.99 (point-focusing), although the original grey matter values were identical in all cortical regions in the model. We have compared the simulated reconstructed images with those obtained by imaging the physical three-dimensional Hoffman brain phantom, which was constructed based upon the same set of data from which the mathematical three-dimensional Hoffman brain model was derived. Although the simulation did not include all of the degrading factors present in the physical imaging, the two images were in good agreement, indicating the applicability of the simulation to a realistic situation and the importance of the detector resolution effect.

A three-dimensional brain phantom has been developed to simulate the activity distributions found in human brain studies currently employed in positron emission tomography (PET). The phantom has a single contiguous chamber and utilizes thin layers of lucite to provide apparent relative concentrations of 5, 1, and 0 for gray matter, white matter, and CSF structures, respectively. The phantom and an ideal image set were created from the same set of data. Thus, the user has a basis for comparing measured images with an ideal set that allows a quantitative evaluation of errors in PET studies with an activity distribution similar to that found in patients. The phantom was employed in a study of the effect of deadtime and scatter on accuracy in quantitation on a current PET system. Deadtime correction factors were found to be significant (1.1-2.5) at count rates found in clinical studies. Deadtime correction techniques were found to be accurate to within 5%. Scatter in emission and attenuation correction data consistently caused 5-15% errors in quantitation, whereas correction for scatter in both types of data reduced errors in accuracy to less than 5%.

13N-labeled ammonia was used to investigate 1) the cerebral extraction and clearance of ammonia, 2) the mechanism by which capillaries accommodate changes in cerebral blood flow (CBF) and 3) its use for the measurement of CBF. The unidirectional extraction of 13NH3 in rhesus monkeys was measured during PaCO2 induced changes in CBF and dog studies were performed using in vitro tissue counting techniques to examine 13NH3 extraction in gray and white matter, mixed tissue and cerebellum during variations in CBF produced by combinations of embolization, local brain compression, and changes in PaCO2. The single pass extraction fraction of 13NH3 varied from about 70 to 20% over a CBF range of 12 to 140 cc/min/100 g. Capillary permeability-surface area product (PS) estimates with a Renkin/Crone model show PS increasing with CBF. The magnitude and rate of increase in PS with CBF was highest in gray matter greater than mixed tissue greater than white matter. Tissue extraction of 13NH3 vs CBF relationship was best described by a unidirectional transport model in which CBF increases by both recruitment of capillaries and by increases of blood velocity in open capillaries. This saturable-recruitment model provides a possible explanation for the mechanism of flow changes at the capillary level. The net 13NH3 extraction subsequent to an i.v. injection increases non-linearly with CBF. Doubling or halving basal CBF produced from 35 to 50% changes in the 13N tissue concentrations with further increases in CBF associated with progressively smaller changes in 13N concentrations.

A new method to measure regional CBF (rCBF) and volume of distribution of water is presented. It centres on recording the tissue build-up and retention of 15O-labelled water during the continuous inhalation of 15O-labelled carbon dioxide. Simultaneously, the arterial concentration is continuously monitored, and corrections for delay and dispersion in the recorded response are made by curve fitting. The values for the volume of distribution of water obtained in four normal subjects were close to reported in vitro values. Using the same fixed distribution volumes for both build-up and steady-state studies resulted in comparable rCBF values for both techniques.

The fluorodeoxyglucose (FDG) method for the measurement of local cerebral metabolic rate of glucose (LCMRGlc) employs typical values of the FDG transport rate constants that have been obtained by kinetic measurements on an appropriate control group. Discrepancies between the true values of the rate constants in tissue and the typical values used in the operational equation of the FDG method will introduce error in the estimate of LCMRGlc. Computer simulations were used to evaluate the accuracy of the FDG method in cases where (1) the tissue LCMRGlc deviates greatly from the normal values (e.g., stroke) or (2) the tissue LCMRGlc changes during the experiment (e.g., epileptic seizure). The effects of the magnitude and duration of metabolic changes were studied. The results indicate that if tissue LCMRGlc differs greatly from the normal value, the error in the estimated LCMRGlc at a scan time of 60 min is less than 20% of the difference between the true and normal values. In the non-steady-state cases, the estimated LCMRGlc was found to be a weighted average of the metabolic rates during the experiments, with the weightings approximately proportional to the plasma FDG concentration at the corresponding times. For example, if LCMRGlc in tissue was 5 times the normal values for the first 10 min but then returned to normal state, the LCMRGlc measured by the FDG method at a scan time of 60 min would be about only 2-3 times the normal value. The results of this study provide a better understanding of the accuracy of the FDG method under various tissue metabolic conditions and is useful for interpreting metabolic values obtained with the FDG method.

Tracer techniques and quantitative autoradiographic and tissue counting models for measurement of metabolic rates were combined with positron computed tomography (PCT) and (F-18)2-fluoro-2-deoxy-D-glucose (FDG) for the measurement of local cerebral metabolic rate for glucose (LCMRGlc) in humans. A three-compartment model, which incorporates hydrolysis of FDG-6-PO4 to FDG, was developed for the measure of kinetic constants and calculation of LCMRGlc. Our model is an extension of that developed by Sokoloff et al. Although small, hydrolysis of FDG-6-PO4 was found to be significant. A PCT system, the ECAT, was used to determine the rate constants, lumped constant, and stability of the model in human beings. The data indicate that cerebral FDG-6-PO4 in humans increases for about 90 minutes, plateaus, and then slowly decreases. After 10 minutes, cerebral blood FDG activity levels were found to be a minor fraction of tissue activity. Precursor pool turnover rate, distribution volumes, and red blood cell-plasma concentration ratios were determined. Reproducibility (precision) of LCMRGlc measurements (approximate 2 cm2 regions) was +/- 5.5% over a 5-hour period. The replacement of arterial blood sampling with venous sampling was validated.

A method for the determination of local cerebral metabolic rates of glucose (LCMRGlc) in normal man is described. The method employs [18F]2-fluoro-2-deoxy-D-glucose (FDG) and emission-computed tomography (ECT). FDG was injected intravenously as a bolus. Radioactivities in separate brain regions were measured with ECT. Plasma FDG concentration following injection was measured from blood samples. A mathematical model that describes the kinetics of FDG transports was employed to determine the transport rate constants of FDG and to convert the radioactivity measurements to metabolic rates. The model has taken into account the possible dephosphorylation reaction from FDG-6-PO4 (FDG-6-P) to free FDG in brain tissues. Experiments were performed in 13 normal volunteers. The rate constants of FDG in man were found to be comparable to those of deoxyglucose in rat and in rhesus monkey. The average LCMRGlc in gray and in white matter were found to be 7.30 +/- 1.18 (SD) and 3.41 +/- 0.64 mg/min per 100 g brain tissue, respectively. The subject-to-subject variation of LCMRGlc as measured by the present method was comparable to those of other methods that measure whole-brain CMRGlc.

The relationship of the mean transit time of the vascular indicator C15O-labeled hemoglobin (tco) and the cerebral blood volume (CBV) as measured by stimulated x-ray fluorescence, to the mean arterial blood pressure (MABP) was examined in rhesus monkeys before and during experiment cerebral seizures. The results demonstrate a marked increase in CBV and a decrease in tco. A substantial portion of these changes is the passive accompaniment of the associated increase in MABP.

The NeuroECAT, a multiplane positron tomograph for imaging the brain, was characterized in terms of both quantitative performance and image quality. The tomograph has four modes of operation, defined by the placement of interplane septa and shadow shields. Each mode was fully characterized by measurement of image resolution, axial resolution, resolution uniformity, scatter, accidentals, and deadtime. Each measurement was performed with scattering media simulating the human head, and resolutions were obtained from images processed with reconstruction techniques actually used in patient imaging. The results for the most frequent mode of operation are: image resolution 9.8 +/- 0.2 mm (FWHM), axial resolution 12.4 +/- 0.4 mm, and scatter 8.1% +/- 0.6. At a count rate of 10,000 cps per image plane, accidentals are 9% and the deadtime 3%. Accidentals are measured and subtracted in hardware, and corrections for deadtime loss are calculated from the on-line measurement of triple-coincidence events. Scatter is estimated from the scan data and subtracted in software. Image quality is demonstrated by phantom studies and by the patient images obtained with [F-18] fluorodeoxyglucose and carbon-11 monoxide. The FDG images show clear delineation of the convolutions of the cortical ribbon, internal gray nuclei, internal and external capsules, and other substructures of the brain. The carbon monoxide images, in addition to visualizing the large vessels, clearly show the blood volumes of the cortex, the Sylvian fissure, and the circle of Willis.