Solutions to common issues in widefield microscopy: vignetting, mosaicing and depth of focus

In this thesis we have developed solutions to common issues regarding widefield microscopes, facing the problem of the intensity inhomogeneity of an image and dealing with two strong limitations: the impossibility of acquiring either high detailed images representative of whole samples or deep 3D objects. First, we cope with the problem of the non-uniform distribution of the light signal inside a single image, named vignetting. In particular we proposed, for both light and fluorescent microscopy, non-parametric multi-image based methods, where the vignetting function is estimated directly from the sample without requiring any prior information. After getting flat-field corrected images, we studied how to fix the problem related to the limitation of the field of view of the camera, so to be able to acquire large areas at high magnification. To this purpose, we developed mosaicing techniques capable to work on-line. Starting from a set of overlapping images manually acquired, we validated a fast registration approach to accurately stitch together the images. Finally, we worked to virtually extend the field of view of the camera in the third dimension, with the purpose of reconstructing a single image completely in focus, stemming from objects having a relevant depth or being displaced in different focus planes. After studying the existing approaches for extending the depth of focus of the microscope, we proposed a general method that does not require any prior information. In order to compare the outcome of existing methods, different standard metrics are commonly used in literature. However, no metric is available to compare different methods in real cases. First, we validated a metric able to rank the methods as the Universal Quality Index does, but without needing any reference ground truth. Second, we proved that the approach we developed performs better in both synthetic and real cases.

The choice of anesthesia influences oxidative energy metabolism and tissue survival in critically ischemic murine skin

In surgical animal studies anesthesia is used regularly. Several reports in the literature demonstrate respiratory and cardiovascular side effects of anesthesiologic agents. The aim of this study was to compare two frequently used anesthesia cocktails (ketamine/xylazine [KX] versus medetomidine/climazolam/fentanyl [MCF]) in skin flap mouse models. Systemic blood values, local metabolic parameters, and surgical outcome should be analyzed in critical ischemic skin flap models. Systemic hypoxia was found in the animals undergoing KX anesthesia compared with normoxia in the MCF group (sO(2): 89.2% +/- 2.4% versus 98.5% +/- 1.2%, P < 0.01). Analysis of tissue metabolism revealed impaired anaerobic oxygen metabolism and increased cellular damage in critical ischemic flap tissue under KX anesthesia (lactate/pyruvate ratio: KX 349.86 +/- 282.38 versus MCF 64.53 +/- 18.63; P < 0.01 and glycerol: KX 333.50 +/- 83.91 micromol/L versus MCF 195.83 +/- 29.49 micromol/L; P < 0.01). After 6 d, different rates of flap tissue necrosis could be detected (MCF 57% +/- 6% versus KX 68% +/- 6%, P < 0.01). In summary we want to point out that the type of anesthesia, the animal model and the goal of the study have to be well correlated. Comparing the effects of KX and MCF anesthesia in mice on surgical outcome was a novel aspect of our study.

Depth of cure of resin composites: is the ISO 4049 method suitable for bulk fill materials?

To evaluate if depth of cure D(ISO) determined by the ISO 4049 method is accurately reflected with bulk fill materials when compared to depth of cure D(new) determined by Vickers microhardness profiles.

Intrapatient reproducibility of the BISxp monitor

BACKGROUND: The Bispectral Index (BIS) reportedly reflects anesthetic depth. It is recommended that anesthetic agents should be titrated to maintain the BIS between 40 and 60 arbitrary BIS units during anesthesia. For anesthesia providers to follow this recommendation, the monitor should be predictably affected by different anesthetic agents and have good interpatient and intrapatient reproducibility. The authors hypothesized that when two BISxp devices (Aspect Medical Systems, Newton, MA) are placed concurrently on the same patient, their readings are concordant throughout the anesthetic period. METHODS: Simultaneous BIS recordings from two BISxp monitors were obtained during anesthesia at 5-s intervals from 12 participants. RESULTS: In total 22,860 concurrent paired BIS readings were obtained. For 10.7% of the time, there were sustained periods of 30 s or greater where the readings suggested a different depth of anesthesia. For 6% of the time, there were sustained periods of 30 s or greater where the readings differed by 10 or more arbitrary BIS units. The regression coefficient (R) for the two devices was 0.65 (range, 0.35-0.92). There was zero bias between the devices, and the 95% limits of agreement ranged between -18 and +17. CONCLUSION: A conflicting anesthetic management was suggested by the simultaneous BIS readings 10.7% of the time. These results suggest that BISxp does not always provide a reproducible single number. Anesthesia providers should not rely exclusively on the BIS reading when assessing depth of anesthesia.

Evaluation of anesthesia recovery quality after low-dose racemic or S-ketamine infusions during anesthesia with isoflurane in horses

OBJECTIVE: To compare anesthesia recovery quality after racemic (R-/S-) or S-ketamine infusions during isoflurane anesthesia in horses. ANIMALS: 10 horses undergoing arthroscopy. PROCEDURES: After administration of xylazine for sedation, horses (n = 5/group) received R-/S-ketamine (2.2 mg/kg) or S-ketamine (1.1 mg/kg), IV, for anesthesia induction. Anesthesia was maintained with isoflurane in oxygen and R-/S-ketamine (1 mg/kg/h) or S-ketamine (0.5 mg/kg/h). Heart rate, invasive mean arterial pressure, and end-tidal isoflurane concentration were recorded before and during surgical stimulation. Arterial blood gases were evaluated every 30 minutes. Arterial ketamine and norketamine enantiomer plasma concentrations were quantified at 60 and 120 minutes. After surgery, horses were kept in a padded recovery box, sedated with xylazine, and video-recorded for evaluation of recovery quality by use of a visual analogue scale (VAS) and a numeric rating scale. RESULTS: Horses in the S-ketamine group had better numeric rating scale and VAS values than those in the R-/S-ketamine group. In the R-/S-ketamine group, duration of infusion was positively correlated with VAS value. Both groups had significant increases in heart rate and mean arterial pressure during surgical stimulation; values in the R-/S-ketamine group were significantly higher than those of the S-ketamine group. Horses in the R-/S-ketamine group required slightly higher end-tidal isoflurane concentration to maintain a surgical plane of anesthesia. Moderate respiratory acidosis and reduced oxygenation were evident. The R-norketamine concentrations were significantly lower than S-norketamine concentrations in the R-/S-ketamine group. CONCLUSIONS AND CLINICAL RELEVANCE: Compared with R-/S-ketamine, anesthesia recovery was better with S-ketamine infusions in horses.

An analysis of variance type method to describe and compare steady states in clinical data

Identifying and comparing different steady states is an important task for clinical decision making. Data from unequal sources, comprising diverse patient status information, have to be interpreted. In order to compare results an expressive representation is the key. In this contribution we suggest a criterion to calculate a context-sensitive value based on variance analysis and discuss its advantages and limitations referring to a clinical data example obtained during anesthesia. Different drug plasma target levels of the anesthetic propofol were preset to reach and maintain clinically desirable steady state conditions with target controlled infusion (TCI). At the same time systolic blood pressure was monitored, depth of anesthesia was recorded using the bispectral index (BIS) and propofol plasma concentrations were determined in venous blood samples. The presented analysis of variance (ANOVA) is used to quantify how accurately steady states can be monitored and compared using the three methods of measurement.

Alfaxalone anesthesia by immersion in oriental fire-bellied toads (Bombina orientalis).

OBJECTIVES To establish an effective alfaxalone concentration to be used for bath immersion of fire-bellied toads (Bombina orientalis) and to describe its effects. STUDY DESIGN Prospective experimental study. ANIMALS Thirteen oriental fire-bellied toads. METHODS The study was carried out in two phases. The pilot phase involved five animals and aimed to identify an alfaxalone concentration capable of producing induction of anesthesia, defined as immobility with a head down position and loss of responsiveness to stimulation with a stick. The following trial in an additional eight toads used the effective alfaxalone concentration established during the pilot phase. Data from 11 animals (three toads in the pilot study and the eight additional toads) were analyzed. Twenty minutes after immersion in the anesthetic solution, the toads were removed from the bath, and heart rate, respiratory rate, the righting, myotactic and the nociceptive withdrawal reflexes were evaluated every 5 minutes. The loss of both righting and nociceptive withdrawal reflexes was considered indicative of a surgical depth of anesthesia. The time elapsed from anesthetic induction to return of righting reflex, the quality of recovery and the occurrence of undesired effects were observed and recorded. RESULTS Immersion was found to be a suitable anesthetic technique for oriental fire-bellied toads and 200 mg L(-1) alfaxalone concentration produced anesthetic induction in 10 out of 11 toads. Side effects, such as skin irritation, erythema and changes in cutaneous pigmentation, were not observed in any animal. The duration of anesthesia ranged from 10 to 30 minutes after removal of the toads from the alfaxalone bath, and surgical depth of anesthesia was never achieved. CONCLUSIONS AND CLINICAL RELEVANCE It was concluded that alfaxalone anesthesia induced by immersion in a concentration of 200 mg L(-1) is only suitable for toads undergoing non-invasive short procedures.

Prestimulus default mode activity influences depth of processing and recognition in an emotional memory task

Low self-referential thoughts are associated with better concentration, which leads to deeper encoding and increases learning and subsequent retrieval. There is evidence that being engaged in externally rather than internally focused tasks is related to low neural activity in the default mode network (DMN) promoting open mind and the deep elaboration of new information. Thus, reduced DMN activity should lead to enhanced concentration, comprehensive stimulus evaluation including emotional categorization, deeper stimulus processing, and better long-term retention over one whole week. In this fMRI study, we investigated brain activation preceding and during incidental encoding of emotional pictures and on subsequent recognition performance. During fMRI, 24 subjects were exposed to 80 pictures of different emotional valence and subsequently asked to complete an online recognition task one week later. Results indicate that neural activity within the medial temporal lobes during encoding predicts subsequent memory performance. Moreover, a low activity of the default mode network preceding incidental encoding leads to slightly better recognition performance independent of the emotional perception of a picture. The findings indicate that the suppression of internally-oriented thoughts leads to a more comprehensive and thorough evaluation of a stimulus and its emotional valence. Reduced activation of the DMN prior to stimulus onset is associated with deeper encoding and enhanced consolidation and retrieval performance even one week later. Even small prestimulus lapses of attention influence consolidation and subsequent recognition performance. Hum Brain Mapp, 2015. © 2015 Wiley Periodicals, Inc.

Design, Calibration, and Evaluation of Depth-of-Interaction-Capable PET Detector Modules

High-resolution, small-bore PET systems suffer from a tradeoff between system sensitivity, and image quality degradation. In these systems long crystals allow mispositioning of the line of response due to parallax error and this mispositioning causes resolution blurring, but long crystals are necessary for high system sensitivity. One means to allow long crystals without introducing parallax errors is to determine the depth of interaction (DOI) of the gamma ray interaction within the detector module. While DOI has been investigated previously, newly available solid state photomultipliers (SSPMs) well-suited to PET applications and allow new modules for investigation. Depth of interaction in full modules is a relatively new field, and so even if high performance DOI capable modules were available, the appropriate means to characterize and calibrate the modules are not. This work presents an investigation of DOI capable arrays and techniques for characterizing and calibrating those modules. The methods introduced here accurately and reliably characterize and calibrate energy, timing, and event interaction positioning. Additionally presented is a characterization of the spatial resolution of DOI capable modules and a measurement of DOI effects for different angles between detector modules. These arrays have been built into a prototype PET system that delivers better than 2.0 mm resolution with a single-sided-stopping-power in excess of 95% for 511 keV g's. The noise properties of SSPMs scale with the active area of the detector face, and so the best signal-to-noise ratio is possible with parallel readout of each SSPM photodetector pixel rather than multiplexing signals together. This work additionally investigates several algorithms for improving timing performance using timing information from multiple SSPM pixels when light is distributed among several photodetectors.