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Quantification of growth in experimental F98 and C6 rat brain tumours was performed on 51 rat brains, 17 of which have been further assessed by 3D tumour reconstruction. Brains were cryosliced and radio-labelled with a ligand of the peripheral type benzodiazepine-receptor (pBR), 3H-Pk11195 [(1-(2-chlorophenyl)-N-methyl-N-(1-methyl-propylene)-3-isoquinoline-carboxamide)] by receptor autoradiography. Manually segmented and automatically registered tumours have been 3D-reconstructed for volumetric comparison on the basis of 3H-Pk11195-based tumour recognition. Furthermore automatically computed areas of −300 μm inner (marginal) zone as well as 300 μm and 600 μm outer tumour space were quantified. These three different regions were transferred onto other adjacent slices that had been labelled by receptor autoradiography with the A1 Adenosine receptor (A1AR)-ligand 3H-CPFPX (3H-8-cyclopentyl-3-(3-fluorpropyl)-1-propylxanthine) for quantitative assessment of A1AR in the three different tumour zones. Hence, a method is described for quantifying various receptor protein systems in the tumour as well as in the marginal invasive zones around experimentally implanted rat brain tumours and their representation in the tumour microenvironment as well as in 3D space. Furthermore, a tool for automatically reading out radio-labelled rat brain slices from auto radiographic films was developed, reconstructed into a consistent 3D-tumour model and the zones around the tumour were visualized. A1AR expression was found to depend upon the tumour volume in C6 animals, but is independent on the time of tumour development. In F98 animals, a significant increase in A1AR receptor protein was found in the Peritumoural zone as a function of time of tumour development and tumour volume.
Purpose: In this trial, we used a previously developed prototype software to assess aesthetic results after reconstructive surgery for congenital breast asymmetry using automated anthropometry. To prove the consensus between the manual and automatic digital measurements, we evaluated the software by comparing the manual and automatic measurements of 46 breasts.
Methods: Twenty-three patients who underwent reconstructive surgery for congenital breast asymmetry at our institution were examined and underwent 3D surface imaging. Per patient, 14 manual and 14 computer-based anthropometric measurements were obtained according to a standardized protocol. Manual and automatic measurements, as well as the previously proposed Symmetry Index (SI), were compared.
Results: The Wilcoxon signed-rank test revealed no significant differences in six of the seven measurements between the automatic and manual assessments. The SI showed robust agreement between the automatic and manual methods.
Conclusion: The present trial validates our method for digital anthropometry. Despite the discrepancy in one measurement, all remaining measurements, including the SI, showed high agreement between the manual and automatic methods. The proposed data bring us one step closer to the long-term goal of establishing robust instruments to evaluate the results of breast surgery.
Volumetric representations of autoradiographic and histological images gain ever more interest as a base to interpret data obtained with /spl mu/-imaging devices like microPET. Beyond supporting spatial orientation within rat brains especially autoradiographic images may serve as a base to quantitatively evaluate the complex uptake patterns of microPET studies with receptor ligands or tumor tracers. They may also serve for the development of rat brain atlases or data models, which can be explored during further image analysis or simulation studies. In all cases a consistent spatial representation of the rat brain, i.e. its anatomy and the corresponding quantitative uptake pattern, is required. This includes both, a restacking of the individual two-dimensional images and the exact registration of the respective volumes. We propose strategies how these volumes can be created in a consistent way and trying to limit the requirements on the circumstances during data acquisition, i.e. being independent from other sources like video imaging of the block face prior to cutting or high resolution micro-X-ray CT or micro MRI.
Virtual training of bone milling requires realtime and realistic haptics of the interaction between the ”virtual mill” and a ”virtual bone”. We propose an exponential abrasion model between a virtual one and the mill bit and combine it with a coarse representation of the virtual bone and the mill shaft for collision detection using the Bullet Physics Engine. We compare our exponential abrasion model to a widely used linear abrasion model and evaluate it quantitatively and qualitatively. The evaluation results show, that we can provide virtual milling in real-time, with an abrasion behavior similar to that proposed in the literature and with a realistic feeling of five different surgeons.
Whole-body PET/CT imaging
(2008)
Aim
Combined whole-body (WB) PET/CT imaging provides better overall co-registration compared to separate CT and PET. However, in clinical routine local PET-CT mis-registration cannot be avoided. Thus, the reconstructed PET tracer distribution may be biased when using the misaligned CT transmission data for CT-based attenuation correction (CT-AC). We investigate the feasibility of retrospective co-registration techniques to align CT and PET images prior to CT-AC, thus improving potentially the quality of combined PET/CT imaging in clinical routine.
Methods
First, using a commercial software registration package CT images were aligned to the uncorrected PET data by rigid and non-rigid registration methods. Co-registration accuracy of both alignment approaches was assessed by reviewing the PET tracer uptake patterns (visual, linked cursor display) following attenuation correction based on the original and co-registered CT. Second, we investigated non-rigid registration based on a prototype ITK implementation of the B-spline algorithm on a similar targeted MR-CT registration task, there showing promising results.
Results
Manual rigid, landmark-based co-registration introduced unacceptable misalignment, in particular in peripheral areas of the whole-body images. Manual, non-rigid landmark-based co-registration prior to CT-AC was successful with minor loco-regional distortions. Nevertheless, neither rigid nor non-rigid automatic co-registration based on the Mutual Information image to image metric succeeded in co-registering the CT and noAC-PET images. In contrast to widely available commercial software registration our implementation of an alternative automated, non-rigid B-spline co-registration technique yielded promising results in this setting with MR-CT data.
Conclusion
In clinical PET/CT imaging, retrospective registration of CT and uncorrected PET images may improve the quality of the AC-PET images. As of today no validated and clinically viable commercial registration software is in routine use. This has triggered our efforts in pursuing new approaches to a validated, non-rigid co-registration algorithm applicable to whole-body PET/CT imaging of which first results are presented here. This approach appears suitable for applications in retrospective WB-PET/CT alignment.
Ziel
Kombinierte PET/CT-Bildgebung ermöglicht verbesserte Koregistrierung von PET- und CT-Daten gegenüber separat akquirierten Bildern. Trotzdem entstehen in der klinischen Anwendung lokale Fehlregistrierungen, die zu Fehlern in der rekonstruierten PET- Tracerverteilung führen können, falls die unregistrierten CT-Daten zur Schwächungskorrektur (AC) der Emissionsdaten verwendet werden. Wir untersuchen daher die Anwendung von Bildregistrierungsalgorithmen vor der CT-basierten AC zur Verbesserung der PET-Aufnahmen.
Methoden
Mittels einer kommerziellen Registrierungssoftware wurden die CT-Daten eines PET/CT- Tomographen durch landmarken- und intensitätsbasierte rigide (starre) und nicht-rigide Registrierungsverfahren räumlich an die unkorrigierten PET-Emissionsdaten angepasst und zur AC verwendet. Zur Bewertung wurden die Tracerverteilungen in den PET-Bildern (vor AC, CT-AC, CT-AC nach Koregistrierung) visuell und mit Hilfe korrelierter Fadenkreuze verglichen. Zusätzlich untersuchten wir die ITK-Implementierung der bekannten B-spline basierten, nicht-rigiden Registrierungsansätze im Hinblick auf ihre Verwendbarkeit für die multimodale PET/CT-Ganzkörperregistrierung.
Ergebnisse
Mittels landmarkenbasierter, nicht-rigider Registrierung konnte die Tracerverteilung in den PET-Daten lokal verbessert werden. Landmarkenbasierte rigide Registrierung führte zu starker Fehlregistrierung in entfernten Körperregionen. Automatische rigide und nicht-rigide Registrierung unter Verwendung der Mutual-Information-Ähnlichkeitsmetrik versagte auf allen verwendeten Datensätzen. Die automatische Registrierung mit B-spline-Funktionen zeigte vielversprechende Resultate in der Anwendung auf einem ähnlich gelagerten CT–MR-Registrierungsproblem.
Fazit
Retrospektive, nicht-rigide Registrierung unkorrigierter PET- und CT-Aufnahmen aus kombinierten Aufnahmensystemen vor der AC kann die Qualität von PET-Aufnahmen im klinischen Einsatz verbessern. Trotzdem steht bis heute im klinischen Alltag keine validierte, automatische Registrierungssoftware zur Verfügung. Wir verfolgen dazu Ansätze für validierte, nicht-rigide Bildregistrierung für den klinischen Einsatz und präsentieren erste Ergebnisse.
Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
Bioimaging of Metals by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS)
(2010)
The distribution analysis of (essential, beneficial, or toxic) metals (e.g., Cu, Fe, Zn, Pb, and others), metalloids, and non‐metals in biological tissues is of key interest in life science. Over the past few years, the development and application of several imaging mass spectrometric techniques has been rapidly growing in biology and medicine. Especially, in brain research metalloproteins are in the focus of targeted therapy approaches of neurodegenerative diseases such as Alzheimer's and Parkinson's disease, or stroke, or tumor growth. Laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS) using double‐focusing sector field (LA‐ICP‐SFMS) or quadrupole‐based mass spectrometers (LA‐ICP‐QMS) has been successfully applied as a powerful imaging (mapping) technique to produce quantitative images of detailed regionally specific element distributions in thin tissue sections of human or rodent brain. Imaging LA‐ICP‐QMS was also applied to investigate metal distributions in plant and animal sections to study, for example, the uptake and transport of nutrient and toxic elements or environmental contamination. The combination of imaging LA‐ICP‐MS of metals with proteomic studies using biomolecular mass spectrometry identifies metal‐containing proteins and also phosphoproteins. Metal‐containing proteins were imaged in a two‐dimensional gel after electrophoretic separation of proteins (SDS or Blue Native PAGE). Recent progress in LA‐ICP‐MS imaging as a stand‐alone technique and in combination with MALDI/ESI‐MS for selected life science applications is summarized.
Signal transmission between different brain regions requires connecting fiber tracts, the structural basis of the human connectome. In contrast to animal brains, where a multitude of tract tracing methods can be used, magnetic resonance (MR)-based diffusion imaging is presently the only promising approach to study fiber tracts between specific human brain regions. However, this procedure has various inherent restrictions caused by its relatively low spatial resolution. Here, we introduce 3D-polarized light imaging (3D-PLI) to map the three-dimensional course of fiber tracts in the human brain with a resolution at a submillimeter scale based on a voxel size of 100 μm isotropic or less. 3D-PLI demonstrates nerve fibers by utilizing their intrinsic birefringence of myelin sheaths surrounding axons. This optical method enables the demonstration of 3D fiber orientations in serial microtome sections of entire human brains. Examples for the feasibility of this novel approach are given here. 3D-PLI enables the study of brain regions of intense fiber crossing in unprecedented detail, and provides an independent evaluation of fiber tracts derived from diffusion imaging data.
Although it has long been presumed that d-amino acids are uncommon in mammalians, substantial amounts of free d-serine have been detected in the mammalian brain. d-Serine has been demonstrated to be an important modulator of glutamatergic neurotransmission and acts as an agonist at the strychnine-insensitive glycine site of N-methyl-d-aspartate receptors. The blood-to-brain transfer of d-serine is thought to be extremely low, and it is assumed that d-serine is generated by isomerization of l-serine in the brain. Stimulated by the observation of a preferred transport of the d-isomer of proline at the blood–brain barrier, we investigated the differential uptake of [3H]-d-serine and [3H]-l-serine in the rat brain 1 h after intravenous injection using quantitative autoradiography. Surprisingly, brain uptake of [3H]-d-serine was significantly higher than that of [3H]-l-serine, indicating a preferred transport of the d-enantiomer of serine at the blood–brain barrier. This finding indicates that exogenous d-serine may have a direct influence on glutamatergic neurotransmission and associated diseases.
GinJinn: An object-detection pipeline for automated feature extraction from herbarium specimens
(2020)
PREMISE:
The generation of morphological data in evolutionary, taxonomic, and ecological studies of plants using herbarium material has traditionally been a labor-intensive task. Recent progress in machine learning using deep artificial neural networks (deep learning) for image classification and object detection has facilitated the establishment of a pipeline for the automatic recognition and extraction of relevant structures in images of herbarium specimens.
METHODS AND RESULTS:
We implemented an extendable pipeline based on state-of-the-art deep-learning object-detection methods to collect leaf images from herbarium specimens of two species of the genus Leucanthemum. Using 183 specimens as the training data set, our pipeline extracted one or more intact leaves in 95% of the 61 test images.
CONCLUSIONS:
We establish GinJinn as a deep-learning object-detection tool for the automatic recognition and extraction of individual leaves or other structures from herbarium specimens. Our pipeline offers greater flexibility and a lower entrance barrier than previous image-processing approaches based on hand-crafted features.
Objective:
Complex hue/saturation images as a new approach for color texture classification using Gabor filters are introduced and compared with common techniques.
Method:
The interpretation of hue and saturationas polar coordinates allows direct use of the HSV-colorspace for Fourier transform. This technique is applied for Gabor feature extraction of color textures. In contrast to other color features based on the RGB-colorspace [1] the combination of color bands is done previous to the filtering.
Results:
The performance of the new HS-featuresis compared with that of RGB based as well as grayscale Gabor features by evaluating the classifi-cation of 30 natural textures. The new HS-featuresshow same results like the best RGB features but allow a more compact representation. On the averagethe color features improve the results of grayscale features.
Conclusion:
The consideration of the color information enhances the classification of color texture. The choice of colorspace cannot be adjudged finally, but the introduced features suggest the use of the HSV-colorspace with less features than RGB.
For accurate registration of histological sections blockface images are frequently used as three dimensional reference. However, due to the use of endocentric lenses the images suffer from perspective errors such as scaling and seemingly relative movement of planes which are located in different distances parallel to the imaging sensor. The suggested correction of those errors is based on the estimation of scaling factors derived from image registration of regions characterized by differing distances to the point of view in neighboring sections. The correction allows the generation of a consistent three dimensional blockface volume.
Whilst considerable progress has been made in enhancing the quality of indirect laryngoscopy and image processing, the evaluation of clinical findings is still based on the clinician's judgement. The aim of this paper was to examine the feasibility of an objective computer-based method for evaluating laryngeal disease. Digitally recorded images obtained by 90 degree- and 70 degree-angled indirect rod laryngoscopy using standardized white balance values were made of 16 patients and 19 healthy subjects. The digital images were evaluated manually by the clinician based on a standardized questionnaire, and suspect lesions were marked and classified on the image. Following colour separation, normal vocal cord areas as well as suspect lesions were analyzed automatically using co-occurrence matrices, which compare colour differences between neighbouring pixels over a predefined distance. Whilst colour histograms did not provide sufficient information for distinguishing between healthy and diseased tissues, consideration of the blue content of neighbouring pixels enabled a correct classification in 81.4% of cases. If all colour channels (red, green and blue) were regarded simultaneously, the best classification correctness obtained was 77.1%. Although only a very basic classification differentiating between healthy and diseased tissue was attempted, the results showed progress compared to grey-scale histograms, which have been evaluated before. The results document a first step towards an objective, machine-based classification of laryngeal images, which could provide the basis for further development of an expert system for use in indirect laryngoscopy.
Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been developed and established as an emerging technique in the generation of quantitative images of metal distributions in thin tissue sections of brain samples (such as human, rat and mouse brain), with applications in research related to neurodegenerative disorders. A new analytical protocol is described which includes sample preparation by cryo-cutting of thin tissue sections and matrix-matched laboratory standards, mass spectrometric measurements, data acquisition, and quantitative analysis. Specific examples of the bioimaging of metal distributions in normal rodent brains are provided. Differences to the normal were assessed in a Parkinson’s disease and a stroke brain model. Furthermore, changes during normal aging were studied. Powerful analytical techniques are also required for the determination and characterization of metal-containing proteins within a large pool of proteins, e.g., after denaturing or non-denaturing electrophoretic separation of proteins in one-dimensional and two-dimensional gels. LA-ICP-MS can be employed to detect metalloproteins in protein bands or spots separated after gel electrophoresis. MALDI-MS can then be used to identify specific metal-containing proteins in these bands or spots. The combination of these techniques is described in the second section.
In order to fix a fracture using minimally invasive surgery approaches, surgeons are drilling complex and tiny bones with a 2 dimensional X-ray as single imaging modality in the operating room. Our novel haptic force-feedback and visual assisted training system will potentially help hand surgeons to learn the drilling procedure in a realistic visual environment. Within the simulation, the collision detection as well as the interaction between virtual drill, bone voxels and surfaces are important. In this work, the chai3d collision detection and force calculation algorithms are combined with a physics engine to simulate the bone drilling process. The chosen Bullet-Physics-Engine provides a stable simulation of rigid bodies, if the collision model of the drill and the tool holder is generated as a compound shape. Three haptic points are added to the K-wire tip for removing single voxels from the bone. For the drilling process three modes are proposed to emulate the different phases of drilling in restricting the movement of a haptic device.
Laryngoscopic images of the vocal tract are used for diagnostic purposes. Quantitative mea-surements like changes of the glottis size or the surface of the vocal cords during an image sequence can be helpful to describe the healing process or to compare the findings of diffe-rent patients. Typically the endoscopic images are circulary symmetric distorted (barrel di-stortion). Therefore measurements of geometric dimensions depend on the object´s position in the image. In this paper an algorithm is presented which allows the computation of the translational invariant "real" object size by correcting the image distortion without using additional calibration of the optical environment.
Evaluierung von Registrierungsstrategien zur multimodalen 3D-Rekonstruktion von Rattenhirnschnitten
(2006)
In dieser Arbeit werden drei Strategien zur 3D Stapelung von multimodalen Schnittbildern vorgestellt. Die Strategien werden experimentell anhand von Dualtracer-Autoradiographien evaluiert. Dazu werden neue Maße zur Beschreibung der Konsistenz innerhalb einer Modalität und der Konsistenz der Modalitäten untereinander entwickelt, die auf bekannten Registrierungsmetriken basieren. Gerade bezüglich der Konsistenz der Modalitäten untereinander zeigen zwei Strategien die besten Resultate: (1) abwechselnde multimodale Registrierung (2) monomodale Rekonstruktion einer Modalität und multimodale 2D Registrierung der zweiten Modalität.