John Aldo Lee

Nonlinear projection with curvilinear distances: Isomap versus curvilinear distance analysis

Dimension reduction techniques are widely used for the analysis and visualization of complex sets of data. This paper compares two recently published methods for nonlinear projection: Isomap and Curvilinear Distance Analysis (CDA). Contrarily to the traditional linear PCA, these methods work like multidimensional scaling, by reproducing in the projection space the pairwise distances measured in the data space. However, they di6er from the classical linear MDS by the metrics they use and by the way they build the mapping (algebraic or neural). While Isomap relies directly on the traditional MDS, CDA is based on a nonlinear variant of MDS, called Curvilinear Component Analysis (CCA). Although Isomap and CDA share the same metric, the comparison highlights their respective strengths and weaknesses.

Quality assessment of dimensionality reduction: Rank-based criteria

Dimensionality reduction aims at providing low-dimensional representations of high-dimensional data sets. Many new nonlinear methods have been proposed for the last years, yet the question of their assessment and comparison remains open. This paper first reviews some of the existing quality measures that are based on distance ranking and K-ary neighborhoods. Next, the definition of the co-ranking matrix provides a tool for comparing the ranks in the initial data set and some low-dimensional embedding. Rank errors and concepts such as neighborhood intrusions and extrusions can then be associated with different blocks of the co-ranking matrix. Several quality criteria can be cast within this unifying framework; they are shown to involve one or several of these characteristic blocks. Following this line, simple criteria are proposed, which quantify two aspects of the embedding quality, namely its overall quality and its tendency to favor intrusions or extrusions. They are applied to several recent dimensionality reduction methods in two experiments, with both artificial and real data.

Segmentation of positron emission tomography images: Some recommendations for target delineation in radiation oncology.

Positron emission tomography can be used in radiation oncology for the delineation of target volumes in the treatment planning stage. Numerous publications deal with this topic and the scientific community has investigated many methodologies, ranging from simple uptake thresholding to very elaborate probabilistic models. Nevertheless, no consensus seems to emerge. This paper reviews delineation techniques that are popular in the literature. Special attention is paid to threshold-based techniques and the caveats of this methodology are pointed out by formal analysis. Next, a simple model of positron emission tomography is suggested in order to shed some light on the difficulties of target delineation and how they might be eventually overcome. Validation aspects are considered as well. Finally, a few recommendations are gathered in the conclusion.

Gradient-based delineation of the primary GTV on FDG-PET in non-small cell lung cancer: A comparison with threshold-based approaches, CT and surgical specimens.

PURPOSE The aim of this study was to validate a gradient-based segmentation method for GTV delineation on FDG-PET in NSCLC through surgical specimen, in comparison with threshold-based approaches and CT. MATERIALS AND METHODS Ten patients with stage I-II NSCLC were prospectively enrolled. Before lobectomy, all patients underwent contrast enhanced CT and gated FDG-PET. Next, the surgical specimen was removed, inflated with gelatin, frozen and sliced. The digitized slices were used to reconstruct the 3D macroscopic specimen. GTVs were manually delineated on the macroscopic specimen and on CT images. GTVs were automatically segmented on PET images using a gradient-based method, a source to background ratio method and fixed threshold values at 40% and 50% of SUV(max). All images were finally registered. Analyses of raw volumes and logarithmic differences between GTVs and GTV(macro) were performed on all patients and on a subgroup excluding the poorly defined tumors. A matching analysis between the different GTVs was also conducted using Dices similarity index. RESULTS Considering all patients, both lung and mediastinal windowed CT overestimated the macroscopy, while FDG-PET provided closer values. Among various PET segmentation methods, the gradient-based technique best estimated the true tumor volume. When analysis was restricted to well defined tumors without lung fibrosis or atelectasis, the mediastinal windowed CT accurately assessed the macroscopic specimen. Finally, the matching analysis did not reveal significant difference between the different imaging modalities. CONCLUSIONS FDG-PET improved the GTV definition in NSCLC including when the primary tumor was surrounded by modifications of the lung parenchyma. In this context, the gradient-based method outperformed the threshold-based ones in terms of accuracy and robustness. In other cases, the conventional mediastinal windowed CT remained appropriate.

Spatial gradients of intracellular calcium in skeletal muscle during fatigue

We have measured the distribution of intracellular calcium concentration in isolated single muscle fibres fromXenopus laevis using the fluorescent calcium indicator fura-2 with digital imaging fluorescence microscopy. Under control conditions, resting and tetanic calcium were uniform throughout a fibre. When fatigue was produced using a prolonged, high-frequency tetanus, the distribution of calcium within muscle fibres became non-uniform, with greater levels near the outer parts of a fibre than near the centre. This non-uniform distribution of calcium was rapidly abolished by lowering the stimulation frequency. When fatigue was produced using a series of repeated intermittent tetani, tetanic calcium showed an initial small increase, followed by a decrease as stimulation was continued. The distribution of calcium remained uniform under these conditions. Calcium distribution was also uniform during recovery from intermittent tetanic stimulation. Although fibres varied considerably in their fatigue resistance, the time for tension to fall to 50% was correlated with the reduction in tetanic calcium seen at this time. These results indicate that there are at least two patterns of reduced calcium release that can contribute to the development of fatigue. The appearance of a calcium gradient is consistent with impaired t-tubular conduction, while a uniform reduction of calcium is likely to be due to the action of metabolic factors on systems controlling calcium homeostasis within the cell.

Changes in tetanic and resting [Ca2+i during fatigue and recovery of single muscle fibres from Xenopus laevis

1. Single muscle fibres were dissected from the toe muscles of Xenopus laevis and microinjected with Fura‐2 to measure myoplasmic calcium concentration ([Ca2+]i). Injected fibres were illuminated at 340 and 380 nm and the ratio of the resulting fluorescence at 505 nm (the Fura‐2 ratio) was taken as a measure of [Ca2+]i. Fibres were fatigued at 21 degrees C by repeated tetani until developed tension had fallen to 50% of control. 2. Tetanic tension declined monotonically during fatiguing stimulation, whereas the tetanic Fura‐2 ratio first increased and then declined. At the 10th tetanus, tension was 87% of control whereas the Fura‐2 ratio was 106% of control. At the end of fatiguing stimulation, where tension was around 50% of control, the tetanic Fura‐2 ratio was reduced to 71%. The rate of decline of both tension and the Fura‐2 ratio after a tetanus slowed during fatigue. During recovery, the tension and the tetanic Fura‐2 ratio recovered in parallel. 3. The resting Fura‐2 ratio increased throughout fatigue reaching 237% of control when tension had declined to 50%. There was a rapid phase of recovery, complete within 1 min, by which time the resting Fura‐2 ratio was 198% of control. Subsequent recovery was slower and took 20‐30 min to reach a stable level which was 121% of control. 4. The resting Fura‐2 ratio towards the end of fatiguing stimulation was greater than the tetanic Fura‐2 ratio in the early part of recovery although there was no detectable increase of resting tension during fatiguing stimulation. This observation suggests that the Ca2+ sensitivity of the contractile proteins was reduced at the end of fatiguing stimulation. 5. Plots of the tetanic tension against tetanic Fura‐2 ratios throughout fatiguing stimulation and recovery also suggested that Ca2+ sensitivity was reduced during fatiguing stimulation when compared to recovery. 6. The increases in resting [Ca2+]i caused by raised [K+]o (from 2.5 to 10 mM) and/or by application of 15% CO2 were much less than those produced by fatiguing stimulation. Much of the elevated [Ca2+]i in fatigue could be reversed by application of dantrolene (25 microM). 7. The results suggest that both reduced tetanic [Ca2+]i and reduced Ca2+ sensitivity contribute to the decline of tension during fatigue.(ABSTRACT TRUNCATED AT 400 WORDS)

Assessment by a deformable registration method of the volumetric and positional changes of target volumes and organs at risk in pharyngo-laryngeal tumors treated with concomitant chemo-radiation

PURPOSE Anatomic changes occur during radiation therapy (RT) for head and neck (H&N) tumors. This study aims at quantifying the volumetric and positional changes of gross tumor volumes (GTV), clinical target volumes (CTV), and organs at risk (OAR). Anatomic (CT) and functional (FDG-PET) imaging were used for the delineation of the GTVs. MATERIALS AND METHODS Ten patients with H&N tumors treated by chemo-RT were used. Contrast-enhanced CT and FDG-PET were acquired prior and during RT following delivery of mean doses of 14.2, 24.5, 35.0, and 44.9 Gy. CT-based GTVs were manually delineated, and PET-based GTVs were segmented using a gradient-based segmentation method. Pre-treatment prophylactic dose CTVs were manually delineated on the pre-treatment CT using consistent and reproducible guidelines. Per-treatment prophylactic CTVs were obtained with an automatic re-contouring method based on deformable registration. For the therapeutic dose CTVs, a 5 mm margin was applied around the corresponding GTVs. OARs such as the parotid glands and the submandibular glands were manually delineated on the pre-treatment CT. OARs on the per-treatment CT were automatically delineated using the method used for prophylactic CTVs. The mean slopes of the relative change in volume over time and the mean displacements of the center of mass after 44.9 Gy were calculated for each volume. RESULTS Regarding volumetric changes, CT-based and PET-based primary tumor GTVs decreased at a mean rate of 3.2% and 3.9%/treatment day (td), respectively; nodal GTVs decreased at a mean rate of 2.2%/td. This led to a corresponding decrease of the CT-based and PET-based therapeutic CTVs by 2.4% and 2.5%/td, respectively. CT- and PET-based prophylactic tumor CTVs decreased by an average of 0.7% and 0.5%/td, respectively. No difference in volume shrinkage was observed between CT- and PET-based volumes. The ipsilateral and contralateral parotid glands showed a mean decrease of 0.9% and 1.0%/td, respectively. The ipsilateral and contralateral submandibular glands shrank at a mean rate of 1.5% and 1.3%/td, respectively. Regarding positional changes, CT-based GTVs showed a lateral shift of 1.3 mm, PET-based GTVs a posterior shift of 3.4mm and the nodal GTVs a medial shift of 1.0 mm, translating into parallel shifts of the therapeutic CTVs. The ipsilateral prophylactic nodal CTV shifted medially by 1.8 mm. The ipsilateral parotid gland shifted medially by 3.4 mm. The ipsilateral submandibular gland showed a medial shift of 1.7 mm and a superior shift of 2.7 mm. The contralateral submandibular gland only showed a superior shift of 1.7 mm. CONCLUSIONS Volumetric and positional changes in TVs and OARs were observed during concomitant chemo-RT suggesting that adaptive strategies, where patients are re-imaged and possibly re-planned during treatment, are worth evaluating.

Radiotherapy for head and neck tumours in 2012 and beyond: conformal, tailored, and adaptive?

Intensity-modulated radiation therapy (IMRT) is a conformal irradiation technique that enables steep dose gradients. In head and neck tumours this approach spares parotid-gland function without compromise to treatment efficacy. Anatomical and molecular imaging modalities may be used to tailor treatment by enabling proper selection and delineation of target volumes and organs at risk, which in turn lead to dose prescriptions that take into account the underlying tumour biology (eg, human papillomavirus status). Therefore, adaptations can be made throughout the course of radiotherapy, as required. Planned dose increases to parts of the target volumes may also be used to match the radiosensitivity of tumours (so-called dose-painting), assessed by molecular imaging. For swift implementation of tailored and adaptive IMRT, tools and procedures, such as accurate image acquisition and reconstruction, automatic segmentation of target volumes and organs at risk, non-rigid image and dose registration, and dose summation methods, need to be developed and properly validated.

Biological image-guided radiotherapy in rectal cancer: Is there a role for FMISO or FLT, next to FDG?

Purpose. The purpose of this study is to investigate the use of PET/CT with fluorodeoxyglucose (FDG), fluorothymidine (FLT) and fluoromisonidazole (FMISO) for radiotherapy (RT) target definition and evolution in rectal cancer. Materials and methods. PET/CT was performed before and during preoperative chemoradiotherapy (CRT) in 15 patients with resectable rectal cancer. PET signals were delineated and CT images on the different time points were non-rigidly registered. Mismatch analyses were carried out to quantify the overlap between FDG and FLT or FMISO tumour volumes (TV) and between PET TVs over time. Results. Ninety sequential PET/CT images were analyzed. The mean FDG, FLT and FMISO-PET TVs showed a tendency to shrink during preoperative CRT. On each time point, the mean FDG-PET TV was significantly larger than the FMISO-PET TV but not significantly larger than the mean FLT-PET TV. There was a mean 65% mismatch between the FMISO and FDG TVs obtained before and during CRT. FLT TVs corresponded better with the FDG TVs (25% mismatch before and 56% during CRT). During CRT, on average 61% of the mean FDG TV (7 cc) overlapped with the baseline mean TV (15.5 cc) (n=15). For FLT, the TV overlap was 49% (n=5) and for FMISO only 20% of the TV during CRT remained inside the contour at baseline (n=10). Conclusion. FDG, FLT and FMISO-PET reflect different functional characteristics that change during CRT in rectal cancer. FLT and FDG show good spatial correspondence, while FMISO seems less reliable due to the non-specific FMISO uptake in normoxic tissue and tracer diffusion through the bowel wall. FDG and FLT-PET/CT imaging seem most appropriate to integrate in preoperative RT for rectal cancer.

Comments on “Comparative Study With New Accuracy Metrics for Target Volume Contouring in PET Image Guided Radiation Therapy”

The impact of PET on radiation therapy is held back by poor methods of defining functional volumes of interest. Many new software tools are being proposed for contouring target volumes but the different approaches are not adequately compared and their accuracy is poorly evaluated due to the illdefinition of ground truth. This paper compares the largest cohort to date of established, emerging and proposed PET contouring methods, in terms of accuracy and variability. We emphasise spatial accuracy and present a new metric that addresses the lack of unique ground truth. 30 methods are used at 13 different institutions to contour functional VOIs in clinical PET/CT and a custom-built PET phantom representing typical problems in image guided radiotherapy. Contouring methods are grouped according to algorithmic type, level of interactivity and how they exploit structural information in hybrid images. Experiments reveal benefits of high levels of user interaction, as well as simultaneous visualisation of CT images and PET gradients to guide interactive procedures. Method-wise evaluation identifies the danger of over-automation and the value of prior knowledge built into an algorithm.