Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Order type dataset analysis for fiducial markers.

ABSTRACT: Order Type (OT) describes a point set avoiding the use of metric information. We show that OT is a descriptor which is invariant to Euclidean geometric transformations, change of scale and perspective projection. In this paper we provide the data related to the application of Order Type with sets of 5, 6, 7, and 8 points to build fiducial markers. The OT is represented through a ? -matrix. We provide the set of points which are suitable to solve directly the point matching, because these have a unique associated ? -matrix. We provide maximal perturbation data for all set of points, maximal perturbation is the radius of the circle, centered in each point in the set, inside which each point can be moved without changing its associated OT. Also we provide the scripts to validate the use of OT in fiducial markers.

SUBMITTER: Cruz Hernandez H

PROVIDER: S-EPMC6139888 | biostudies-other | 2018 Oct

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Order type dataset analysis for fiducial markers.

Cruz Hernández Heriberto H de la Fraga Luis Gerardo LG

Data in brief 20180831

Order Type (OT) describes a point set avoiding the use of metric information. We show that OT is a descriptor which is invariant to Euclidean geometric transformations, change of scale and perspective projection. In this paper we provide the data related to the application of Order Type with sets of 5, 6, 7, and 8 points to build fiducial markers. The OT is represented through a λ -matrix. We provide the set of points which are suitable to solve directly the point matching, because these have a ...[more]

PMID: 30225323

Similar Datasets

Enhancement of RGB-D Image Alignment Using Fiducial Markers.

Project description:Three-dimensional (3D) reconstruction methods generate a 3D textured model from the combination of data from several captures. As such, the geometrical transformations between these captures are required. The process of computing or refining these transformations is referred to as alignment. It is often a difficult problem to handle, in particular due to a lack of accuracy in the matching of features. We propose an optimization framework that takes advantage of fiducial markers placed in the scene. Since these markers are robustly detected, the problem of incorrect matching of features is overcome. The proposed procedure is capable of enhancing the 3D models created using consumer level RGB-D hand-held cameras, reducing visual artefacts caused by misalignments. One problem inherent to this solution is that the scene is polluted by the markers. Therefore, a tool was developed to allow their removal from the texture of the scene. Results show that our optimization framework is able to significantly reduce alignment errors between captures, which results in visually appealing reconstructions. Furthermore, the markers used to enhance the alignment are seamlessly removed from the final model texture.

| S-EPMC7085533 | biostudies-literature

Minimal Inter-Fractional Fiducial Migration during Image-Guided Lung Stereotactic Body Radiotherapy Using SuperLock Nitinol Coil Fiducial Markers.

Project description:ObjectivesStereotactic body radiotherapy (SBRT) is being increasingly used for the treatment of patients with lung cancer or lung metastasis who are medically unfit to undergo resection. In order to improve accuracy and confidence in targeting tumors, many centers rely on fiducial implantation. We evaluated the migration of a novel fiducial marker specifically designed for lung tissue implanted via electromagnetic navigation bronchoscopy (ENB).MethodsWe retrospectively quantified the individual and group migrations of SuperLock nitinol coil fiducials for 15 patients receiving lung stereotactic body radiotherapy (SBRT), in order to evaluate the reliability of using these fiducials as a target surrogate for cases where tumors cannot be clearly delineated on cone beam CTs (CBCTs). For each fraction, we compared the individual and group migrations of the fiducials between the planning CT and the acquired CBCT. The group migration was defined as the distance between the centroids of the fiducial group and GTV.ResultsA total of 16 lung targets were included in our study for these 15 patients (one patient with two targets). Of 55 fiducials placed, we observed a 100% retention rate. The mean individual migration was 1.87 mm (range, 0.63-5.25 mm) with a standard deviation of 1.26 mm. The mean group migration was 1.94 mm (range, 0.03-6.19 mm) with a standard deviation of 1.45 mm. Overall, there was minimal change in the relative locations of the markers with respect to each other, as well as to the target.ConclusionsWe found that the SuperLock nitinol coil fiducial marker positions are stable throughout the radiation treatment, and can be used as a reliable surrogate to target, and to avoid geometric misses during gated treatments.

| S-EPMC4497733 | biostudies-literature

Fiducial markers for combined 3-dimensional mass spectrometric and optical tissue imaging.

Project description:Mass spectrometric imaging (MSI) has become widely used in the analysis of a variety of biological surfaces. Biological samples are spatially, morphologically, and metabolically complex. Multimodal molecular imaging is an emerging approach that is capable of dealing with this complexity. In a multimodal approach, different imaging modalities can provide precise information about the local molecular composition of the surfaces. Images obtained by MSI can be coregistered with images obtained by other molecular imaging techniques such as microscopic images of fluorescent protein expression or histologically stained sections. In order to properly coregister images from different modalities, each tissue section must contain points of reference, which are visible in all data sets. Here, we report a newly developed coregistration technique using fiducial markers such as cresyl violet, Ponceau S, and bromophenol blue that possess a combination of optical and molecular properties that result in a clear mass spectrometric signature. We describe these fiducial markers and demonstrate an application that allows accurate coregistration and 3-dimensional reconstruction of serial histological and fluorescent microscopic images with MSI images of thin tissue sections from a breast tumor model.

| S-EPMC3302962 | biostudies-literature

Fiducial markers visibility and artefacts in prostate cancer radiotherapy multi-modality imaging.

Project description:BACKGROUND:In this study, a novel pelvic phantom was developed and used to assess the visibility and presence of artefacts from different types of commercial fiducial markers (FMs) on multi-modality imaging relevant to prostate cancer. METHODS AND MATERIALS:The phantom was designed with 3D printed hollow cubes in the centre. These cubes were filled with gel to mimic the prostate gland and two parallel PVC rods were used to mimic bones in the pelvic region. Each cube was filled with gelatine and three unique FMs were positioned with a clinically-relevant spatial distribution. The FMs investigated were; Gold Marker (GM) CIVCO, GM RiverPoint, GM Gold Anchor (GA) line and ball shape, and polymer marker (PM) from CIVCO. The phantom was scanned using several imaging modalities typically used to image prostate cancer patients; MRI, CT, CBCT, planar kV-pair, ExacTrac, 6MV, 2.5MV and integrated EPID imaging. The visibility of the markers and any observed artefacts in the phantom were compared to in-vivo scans of prostate cancer patients with FMs. RESULTS:All GMs were visible in volumetric scans, however, they also had the most visible artefacts on CT and CBCT scans, with the magnitude of artefacts increasing with FM size. PM FMs had the least visible artefacts in volumetric scans but they were not visible on portal images and had poor visibility on lateral kV images. The smallest diameter GMs (GA) were the most difficult GMs to identify on lateral kV images. CONCLUSION:The choice between different FMs is also dependent on the adopted IGRT strategy. PM was found to be superior to investigated gold markers in the most commonly used modalities in the management of prostate cancer; CT, CBCT and MRI imaging.

| S-EPMC6933910 | biostudies-literature

EUS-guided placement of fiducial markers for the treatment of pancreatic cancer.

Project description: Not available

| S-EPMC6731123 | biostudies-literature

Radiopaque drug-eluting embolisation beads as fiducial markers for stereotactic liver radiotherapy.

Project description:ObjectiveTo determine the feasibility of using radiopaque (RO) beads as direct tumour surrogates for image-guided radiotherapy (IGRT) in patients with liver tumours after transarterial chemoembolisation (TACE).MethodsA novel vandetanib-eluting RO bead was delivered via TACE as part of a first-in-human clinical trial in patients with either hepatocellular carcinoma or liver metastases from colorectal cancer. Following TACE, patients underwent simulated radiotherapy imaging with four-dimensional computed tomography (4D-CT) and cone-beam CT (CBCT) imaging. RO beads were contoured using automated thresholding, and feasibility of matching between the simulated radiotherapy planning dataset (AVE-IP image from 4D data) and CBCT scans assessed. Additional kV, MV, helical CT and CBCT images of RO beads were obtained using an in-house phantom. Stability of RO bead position was assessed by comparing 4D-CT imaging to CT scans taken 6-20 days following TACE.ResultsEight patients were treated and 4D-CT and CBCT images acquired. RO beads were visible on 4D-CT and CBCT images in all cases and matching successfully performed. Differences in centre of mass of RO beads between CBCT and simulated radiotherapy planning scans (AVE-IP dataset) were 2.0 mm mediolaterally, 1.7 mm anteroposteriorally and 3.5 mm craniocaudally. RO beads in the phantom were visible on all imaging modalities assessed. RO bead position remained stable up to 29 days post TACE.ConclusionRO beads are visible on IGRT imaging modalities, showing minimal artefact. They can be used for on-set matching with CBCT and remain stable over time.Advances in knowledgeThe role of RO beads as fiducial markers for stereotactic liver radiotherapy is feasible and warrants further exploration as a combination therapy approach.

| S-EPMC8822567 | biostudies-literature

Automatic Calibration of an Industrial RGB-D Camera Network Using Retroreflective Fiducial Markers.

Project description:This paper describes a non-invasive, automatic, and robust method for calibrating a scalable RGB-D sensor network based on retroreflective ArUco markers and the iterative closest point (ICP) scheme. We demonstrate the system by calibrating a sensor network comprised of six sensor nodes positioned in a relatively large industrial robot cell with an approximate size of 10 x 10 x 4 m . Here, the automatic calibration achieved an average Euclidean error of 3 c m at distances up to 9 . 45 m . To achieve robustness, we apply several innovative techniques: Firstly, we mitigate the ambiguity problem that occurs when detecting a marker at long range or low resolution by comparing the camera projection with depth data. Secondly, we use retroreflective fiducial markers in the RGB-D calibration for improved accuracy and detectability. Finally, the repeating ICP refinement uses an exact region of interest such that we employ the precise depth measurements of the retroreflective surfaces only. The complete calibration software and a recorded dataset are publically available and open source.

| S-EPMC6479303 | biostudies-literature

Convex probe endobronchial ultrasound placement of fiducial markers for central lung nodule (with video).

Project description: Not available

| S-EPMC4445176 | biostudies-literature

<i>In situ</i> fiducial markers for 3D correlative cryo-fluorescence and FIB-SEM imaging.

Project description:Imaging of cells and tissues has improved significantly over the last decade. Dual-beam instruments with a focused ion beam mounted on a scanning electron microscope (FIB-SEM), offering high-resolution 3D imaging of large volumes and fields-of-view are becoming widely used in the life sciences. FIB-SEM has most recently been implemented on fully hydrated, cryo-immobilized, biological samples. Correlative light and electron microscopy workflows combining fluorescence microscopy (FM) with FIB-SEM imaging exist, whereas workflows combining cryo-FM and cryo-FIB-SEM imaging are not yet commonly available. Here, we demonstrate that fluorescently labeled lipid droplets can serve as in situ fiducial markers for correlating cryo-FM and FIB-SEM datasets and that this approach can be used to target the acquisition of large FIB-SEM stacks spanning tens of microns under cryogenic conditions. We also show that cryo-FIB-SEM imaging is particularly informative for questions related to organelle structure and inter-organellar contacts, nuclear organization, and mineral deposits in cells.

| S-EPMC8253967 | biostudies-literature

Fiducial markers for stereotactic lung radiation therapy: review of the transthoracic, endovascular and endobronchial approaches.

Project description:Stereotactic body radiation therapy is an alternative to surgery for early-stage, inoperable peripheral non-small cell lung cancer. As opposed to linear accelerator (linac)-based (e.g. gating) and free-breathing techniques, CyberKnife® with Synchrony® technology allows accurate radiation delivery by means of a real-time respiratory motion tracking system using, in most cases, metal fiducial markers (FMs) placed in the vicinity of the target. The aims of this review are as follows. First, to describe the safety and efficacy of the transthoracic, endovascular and endobronchial FM insertion techniques for peripheral pulmonary lesions (PPLs). Second, to analyse performance in terms of the migration and tracking rates of different FM types. Recent developments in FM tracking for central lesions will also be reviewed. In conclusion, for PPLs, the endobronchial approach provides a low rate of pneumothorax, offers the possibility of concurrent diagnostic sampling for both the PPL and the lymph nodes, and, finally, reduces the intervention time compared to other techniques. In this context, coil-tailed and coil-spring FMs have shown the lowest migration rate with a consequently high tracking rate.

| S-EPMC9488911 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data