IODeep: An IOD for the introduction of deep learning in the DICOM standard

BACKGROUND AND OBJECTIVE

In recent years, Artificial Intelligence (AI) and in particular Deep Neural Networks (DNN) became a relevant research topic in biomedical image segmentation due to the availability of more and more data sets along with the establishment of well known competitions. Despite the popularity of DNN based segmentation on the research side, these techniques are almost unused in the daily clinical practice even if they could support effectively the physician during the diagnostic process. Apart from the issues related to the explainability of the predictions of a neural model, such systems are not integrated in the diagnostic workflow, and a standardization of their use is needed to achieve this goal.

METHODS

This paper presents IODeep a new DICOM Information Object Definition (IOD) aimed at storing both the weights and the architecture of a DNN already trained on a particular image dataset that is labeled as regards the acquisition modality, the anatomical region, and the disease under investigation.

RESULTS

The IOD architecture is presented along with a DNN selection algorithm from the PACS server based on the labels outlined above, and a simple PACS viewer purposely designed for demonstrating the effectiveness of the DICOM integration, while no modifications are required on the PACS server side. Also a service based architecture in support of the entire workflow has been implemented.

CONCLUSION

IODeep ensures full integration of a trained AI model in a DICOM infrastructure, and it is also enables a scenario where a trained model can be either fine-tuned with hospital data or trained in a federated learning scheme shared by different hospitals. In this way AI models can be tailored to the real data produced by a Radiology ward thus improving the physician decision making process. Source code is freely available at https://github.com/CHILab1/IODeep.git.

Telehealth modulation and new proposals during the Covid-19 pandemic: a literature review

The Covid-19 pandemic has completely modified the Healthcare organization. This review aims to analyze the evolution of the different Telemedicine areas during pandemic. Electronic Health Records allows accelerating the study of patients suffering from Covid-19 disease, supporting their clinical assistance. The decreasing rehabilitation programs have determined a deterioration of the patient quality of life. Teleradiology was necessary to discard the increased requests and dab the shortage of staff, and to guarantee the interaction between specialist and patient. Telecardiology was fundamental determining a reduced of secondary mortality for cardiological complications of the infection. Teledermatology has permitted an early identification of the patients affected through diagnoses of cutaneous signs, reducing clinical visits. Telelegal-medicine changed through a law, that was introduced allowing a remarkable use of videoconferencing in the different stages of judicial and extrajudicial process. The digital consultations and home drug delivery were implemented in telepharmacy area. Artificial Intelligence allows an early diagnosis of the infection, monitoring the treatment through an intelligent platform. Robotic assisted telemedicine minimizes the risk of exposure allowing the disinfection of the places, drugs and meals delivery, the measurement of vital signs. Mobile Health facilitated the collection and the automatic transfer of the patient's parameters. Telemedicine would constitute still today as complementary but not substitutive to the traditional medicine. During the pandemic telemedicine has resulted important to guarantee continuity cures. Radiology and Dermatology showed a major telemedicine application.

Blood Vessel Detection Algorithm for Tissue Engineering and Quantitative Histology

Immunohistochemistry for vascular network analysis plays a fundamental role in basic science, translational research and clinical practice. However, identifying vascularization in histological tissue images is time consuming and markedly depends on the operator’s experience. In this study, we present “blood vessel detection—BVD”, an automatic algorithm for quantitative analysis of blood vessels in immunohistochemical images. BVD is based on extraction and analysis of low-level image features and spatial filtering techniques, which do not require a training phase. BVD algorithm performance was comparatively evaluated on histological sections from three different in vivo experiments. Collectively, 173 independent images were analyzed, and the algorithm's results were compared to those obtained by human operators. The developed BVD algorithm proved to be a robust and versatile tool, being able to quantify number, area, and spatial distribution of blood vessels within all three considered histologic datasets. BVD is provided as an open-source application working on different operating systems. BVD is supported by a user-friendly graphical interface designed to facilitate large-scale analysis.

Convolutional architectures for virtual screening

Background

A Virtual Screening algorithm has to adapt to the different stages of this process. Early screening needs to ensure that all bioactive compounds are ranked in the first positions despite of the number of false positives, while a second screening round is aimed at increasing the prediction accuracy.

Results

A novel CNN architecture is presented to this aim, which predicts bioactivity of candidate compounds on CDK1 using a combination of molecular fingerprints as their vector representation, and has been trained suitably to achieve good results as regards both enrichment factor and accuracy in different screening modes (98.55% accuracy in active-only selection, and 98.88% in high precision discrimination).

Conclusion

The proposed architecture outperforms state-of-the-art ML approaches, and some interesting insights on molecular fingerprints are devised.

A tunable digital ishihara plate for pre-school aged children

Colors play a fundamental role for children, both in the everyday life and in education. They recognize the surrounding world, and play games making a large use of colors. They learn letters and numbers by means of colors. As a consequence, early diagnosis of color blindness is an crucial to support an individual affected by this visual perception alteration at the initial phase of his/her life. The diagnosis of red-green color deficiencies (protanopia or deuteranopia) is commonly accomplished by means of the Ishihara test, which consists of plates showing dots with different sizes where some of them compose numbers within a gamut of colors while the ones composing the background have different colors. In this paper, a web application written in javascript is presented, that implements a digital Ishihara-like test for pre-school aged children. Instead numbers or letters, It can transform any binary image representing animal shapes, or any other child-friendly shape, into an Ishihara-like image. This digital plate is not static. The operator can increment the dot density to improve the quality of the shape contour and the entire plate can be redrawn with different dot sizes/colors chosen randomly according to the color pattern of the test. Separate controls for brightness and saturation are implemented to calibrate the chromatic aspect of the background and foreground dots.

A teledentistry system for the second opinion

In this paper we present a Teledentistry system aimed to the Second Opinion task. It make use of a particular camera called intra-oral camera, also called dental camera, in order to perform the photo shooting and real-time video of the inner part of the mouth. The pictures acquired by the Operator with such a device are sent to the Oral Medicine Expert (OME) by means of a current File Transfer Protocol (FTP) service and the real-time video is channeled into a video streaming thanks to the VideoLan client/server (VLC) application. It is composed by a HTML5 web-pages generated by PHP and allows to perform the Second Opinion both when Operator and OME are logged and when one of them is offline.

Automatic skull stripping in MRI based on morphological filters and fuzzy c-means segmentation

In this paper a new automatic skull stripping method for T1-weighted MR image of human brain is presented. Skull stripping is a process that allows to separate the brain from the rest of tissues. The proposed method is based on a 2D brain extraction making use of fuzzy c-means segmentation and morphological operators applied on transversal slices. The approach is extended to the 3D case, taking into account the result obtained from the preceding slice to solve the organ splitting problem. The proposed approach is compared with BET (Brain Extraction Tool) implemented in MRIcro software.

Reports of the AAAI 2010 Fall Symposia

The Association for the Advancement of Artificial Intelligence was pleased to present the 2010 Fall Symposium Series, held Thursday through Saturday, November 11-13, at the Westin Arlington Gateway in Arlington, Virginia. The titles of the eight symposia are as follows: (1) Cognitive and Metacognitive Educational Systems; (2) Commonsense Knowledge; (3) Complex Adaptive Systems: Resilience, Robustness, and Evolvability; (4) Computational Models of Narrative; (5) Dialog with Robots; (6) Manifold Learning and Its Applications; (7) Proactive Assistant Agents ; and (8) Quantum Informatics for Cognitive, Social, and Semantic Processes. The highlights of each symposium are presented in this report.

Reports of the AAAI 2009 Fall Symposia

The Association for the Advancement of Artificial Intelligence was pleased to present the 2009 Fall Symposium Series, held Thursday through Saturday, November 5–7, at the Westin Arlington Gateway in Arlington, Virginia. The Symposium Series was preceded on Wednesday, November 4 by a one-day AI funding seminar. The titles of the seven symposia were as follows: (1) Biologically Inspired Cognitive Architectures, (2) Cognitive and Metacognitive Educational Systems, (3) Complex Adaptive Systems and the Threshold Effect: Views from the Natural and Social Sciences, (4) Manifold Learning and Its Applications, (5) Multirepresentational Architectures for Human-Level Intelligence, (6) The Uses of Computational Argumentation, and (7) Virtual Healthcare Interaction.

Multislice human organ extraction based on GVF

Segmentation techniques based on active contours algorithm are widely used in medical imaging. Unfortunately, they require a lot of parameters to be used and this can represent an issue for those physicians with not much informatics skills. This paper proposes a software tool which allows to segment multiple slice can differ organ extraction setting a small number of parameters. Moreover, the tool offers the functionality to perform a multiple segmentation the same time, so that an entire volume composed by hundreds slices can be segmented.

Pervasive access to MRI bias artifact suppression service on a grid

Bias artifact corrupts MRIs in such a way that the image is afflicted by illumination variations. Some of the authors proposed the exponential entropy-driven homomorphic unsharp masking ( E(2)D-HUM) algorithm that corrects this artifact without any a priori hypothesis about the tissues or the MRI modality. Moreover, E(2)D-HUM does not care about the body part under examination and does not require any particular training task. People who want to use this algorithm, which is Matlab-based, have to set their own computers in order to execute it. Furthermore, they have to be Matlab-skilled to exploit all the features of the algorithm. In this paper, we propose to make such algorithm available as a service on a grid infrastructure, so that people can use it almost from everywhere, in a pervasive fashion, by means of a suitable user interface running on smartphones. The proposed solution allows physicians to use the E(2)D-HUM algorithm (or any other kind of algorithm, given that it is available as a service on the grid), being it remotely executed somewhere in the grid, and the results are sent back to the user's device. This way, physicians do not need to be aware of how to use Matlab to process their images. The pervasive service provision for medical image enhancement is presented, along with some experimental results obtained using smartphones connected to an existing Globus-based grid infrastructure.

Bias artifact suppression on MR volumes

RF-inhomogeneity correction is a relevant research topic in the field of magnetic resonance imaging (MRI). A volume corrupted by this artifact exhibits nonuniform illumination both inside a single slice and between adjacent ones. In this work a bias correction technique is presented, which suppresses this artifact on MR volumes scanned from different body parts without any a priori hypothesis on the artifact model. Theoretical foundations of the method are reported together with experimental results and a comparison is presented with both the 2D version of the algorithm and other techniques that are widely used in MRI literature.

Blood vessels and feature points detection on retinal images

In this paper we present a method for the automatic extraction of blood vessels from retinal images, while capturing points of intersection/overlap and endpoints of the vascular tree. The algorithm performance is evaluated through a comparison with handmade segmented images available on the STARE project database (STructured Analysis of the REtina). The algorithm is performed on the green channel of the RGB triad. The green channel can be used to represent the illumination component. The matched filter is used to enhance vessels w.r.t. the background. The separation between vessels and background is accomplished by a threshold operator based on gaussian probability density function. The length filtering removes pixels and isolated segments from the resulting image. Finally endpoints, intersections and overlapping vessels are extracted.

Exponential Entropy Driven HUM on Knee MR Images

A very important artifact corrupting Magnetic Resonance Images is the RF inhomogeneity. This kind of artifact generates variations of illumination which trouble both direct examination by the doctor and segmentation algorithms. Even if homomorphic filtering approaches have been presented in literature, none of them has developed a measure to determine the cut-off frequency. In this work we present a measure based on information theory with a large experimental setup aimed to demonstrate the validity of our approach.

A Gabor-based technique for bias removal in MR images

Magnetic Resonance images are often characterized by irregularly displaced luminance fluctuations that are called bias artifact. This disturb is due to a drop in signal intensity caused by the distance between imaged sample and receiver coil. An original approach to bias removal in Magnetic Resonance images is presented, which is based on the use of Gabor filter to extract the artifact. The proposed technique restores the image using a correction model, which is derived from the attenuation of signal diffusion across the tissues. No hypotheses are made about the structure of the tissues under investigation and the used MR spectrum. The approach is presented in detail, and extensive experimental results are reported along with a comparison with other popular techniques for bias removal.

Illumination Correction on MR Images

OBJECTIVE

An important artifact corrupting Magnetic Resonance Images is the rf inhomogeneity, also called bias artifact. This anomaly produces an abnormal illumination fluctuation on the image, due to variations of the device magnetic field. This artifact is particularly strong on images acquired with a device specialized on upper and lower limbs due to their coil configuration. A method based on homomorphic filtering aimed to suppress this artifact was proposed by Guillemaud. This filter has two faults: it doesn't provide an indication about the cutoff frequency (cf) and introduces another illumination artifact on the edges of the foreground. This work is an improvement to this method because it resolves both problems.

METHODS

The experimental setup has been performed on knee images obtained by 5 volunteers and acquired through an Artoscan device using the following parameters: Spin Echo sequence, Repetition time: 980 ms, Echo time: 26 ms, Slice thickness: 4 mm, Flip Angle: 90 degrees .

RESULTS

Two specialists in orthoptics evaluated the results of the proposed approach by examining the restored images and validating the results produced by the filter. A quantitative evaluation has been performed on a manually segmented restored image using the coefficient of variation (cv) measure.

CONCLUSIONS

Following the specialists qualitative evaluation, the illuminance of upper and lower peripheral zones results to be enhanced; a loose of contrast can be noted only in few cases. The Bias image exhibits an artifact focused usually on the central part of the foreground. The quantitative evaluation based on cv shows that this index is lowered for all the segmented regions with respect to the original value. The method is automatic and doesn't require any hypothesis on the tissues. A manual version of the algorithm can be also implemented allowing the physician to choose the preferred cf. In this case the value selected by the method can be considered as a default value.

Morphological exponential entropy driven-HUM

This paper presents an improvement to the exponential entropy driven-homomorphic unsharp masking (E(2)D-HUM) algorithm devoted to illumination artifact suppression on magnetic resonance images. E(2)D-HUM requires a segmentation step to remove dark regions in the foreground whose intensity is comparable with background, because strong edges produce streak artifacts on the tissues. This new version of the algorithm keeps the same good properties of E(2)D-HUM without a segmentation phase, whose parameters should be chosen in relation to the image.

Usefulness of a comprehensive neurophysiological assessment for early diagnosis and prognosis of traumatic brachial plexus injuries

PURPOSE

To illustrate how a thorough neurophysiological evaluation allows early diagnosis and prognosis of traumatic brachial plexus injuries.

METHODS

As examples, we report on the case of two patients with acute traumatic brachial plexus injuries for whom a comprehensive neurophysiological evaluation allowed early diagnosis and prognosis.

RESULTS

Neurophysiological findings were consistent with complete proximal (root) lesion in one patient and a severe neuroapraxic block between Erb point and axilla in the other one.

CONCLUSIONS

The two reported acute cases of traumatic brachial plexus injuries demonstrated the high diagnostic and prognostic value of the neurophysiological tests when fully utilized.

Three-dimensional geometrical models of the inguinal region. Towards a new stereology

In this work we studied the inguinal-abdominal region and the inguinal canal using three-dimensional geometrical models. We built the models through computer aided geometric modeling techniques on the basis of observations during real dissections, operations and diagnostic medical imaging. The obtained models show in a complete modular synthesis and with a schematic iconology the structural organization of the anatomical districts in a logic sequence of layers and topographic and spatial relationships among its components. The models represent an amazing support to anatomy and clinical anatomy for teaching and research purposes on organogenesis, surgery and diagnosis.

Development of software in the study of carotid artery in the neck

The aim of this work was to develop and employ software for the study of the common carotid artery and its branches in the neck. We first constructed geometric models of anatomic components, for the building of knowledge bases to be used in automatic feature extraction techniques from images. Then, we developed a software system characterised by three-dimensional visualisation, image processing functions, knowledge base and a programming language to describe classification processing by means of fuzzy logic. The software system was used to perform automatic reconstruction of three-dimensional models of carotid arteries from contiguous CT scans of the neck. These findings suggest that such software systems represent a useful help in the study of image based diagnosis of carotid arteries.

[Intracranial mycotic aneurysms. Considerations apropos of 2 clinical cases]

Authors refer about the pathogenesis, the clinical and therapeutical problems, concerning two patients affected by mycotic intracranial aneurysms. They describe the anamnestical data of M.I.A., the clinic, the diagnostical and therapeutical measures in use.

Intrasacral meningocele associated to lumbar disk rupture. A case report

A case of intrasacral meningocele associated to L4-L5 discal rupture is described. The possibility for this kind of malformation to be asymptomatic is emphasized.

Recurrent massive otorrhagia caused by a petrous carotid aneurysm

Aneurysms of the petrous portion of the internal carotid artery are quite rare lesions. The case of a 60-year-old man who showed recurrent spontaneous otorrhagia caused by a petrous carotid aneurysm of considerable size is reported here. Mycotic origin of the lesion is presumed. Common carotid ligation was effective in resolving bleeding and did not cause any permanent neurological deficit. Other surgical procedures are acceptable.