We present Clinica (www.clinica.run), an open-source software platform designed to make clinical neuroscience studies easier and more reproducible. Clinica aims for researchers to (i) spend less time on data management and processing, (ii) perform reproducible evaluations of their methods, and (iii) easily share data and results within their institution and with external collaborators. The core of Clinica is a set of automatic pipelines for processing and analysis of multimodal neuroimaging data (currently, T1-weighted MRI, diffusion MRI, and PET data), as well as tools for statistics, machine learning, and deep learning. It relies on the brain imaging data structure (BIDS) for the organization of raw neuroimaging datasets and on established tools written by the community to build its pipelines. It also provides converters of public neuroimaging datasets to BIDS (currently ADNI, AIBL, OASIS, and NIFD). Processed data include image-valued scalar fields (e.g., tissue probability maps), meshes, surface-based scalar fields (e.g., cortical thickness maps), or scalar outputs (e.g., regional averages). These data follow the ClinicA Processed Structure (CAPS) format which shares the same philosophy as BIDS. Consistent organization of raw and processed neuroimaging files facilitates the execution of single pipelines and of sequences of pipelines, as well as the integration of processed data into statistics or machine learning frameworks. The target audience of Clinica is neuroscientists or clinicians conducting clinical neuroscience studies involving multimodal imaging, and researchers developing advanced machine learning algorithms applied to neuroimaging data.
Access to the scene irradiance is a desirable feature in many computer vision algorithms. Applications like BRDF estimation, relighting or augmented reality need measurements of the object's photometric properties and the simplest method to get them is using a camera. However, the first step necessary to achieve this goal is the computation of the function that relates scene irradiance to image intensities. In this paper we propose to exploit the large variety of an object's appearances in photo collections to recover this non linear function for each of the cameras that acquired the available images. This process, also known as radiometric calibration, uses an unstructured set of images, to recover the camera's geometric calibration and a 3D scene model, using available methods. From this input, the camera response function is estimated for each image. This highly ill-posed problem is made tractable by using appropriate priors. The proposed approach is based on the empirical prior on camera response functions introduced by Grossberg and Nayar. Linear methods are proposed that allow to compute approximate solutions, which are then refined by non-linear least squares optimization.
Abstract. We address the problem of jointly estimating the scene illumination, the radiometric camera calibration and the reflectance properties of an object using a set of images from a community photo collection. The highly ill-posed nature of this problem is circumvented by using appropriate representations of illumination, an empirical model for the nonlinear function that relates image irradiance with intensity values and additional assumptions on the surface reflectance properties. Using a 3D model recovered from an unstructured set of images, we estimate the coefficients that represent the illumination for each image using a frequency framework. For each image, we also compute the corresponding camera response function. Additionally, we calculate a simple model for the reflectance properties of the 3D model. A robust non-linear optimization is proposed exploiting the high sparsity present in the problem.
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