Explaining deep learning models in a way that humans can easily understand is essential for responsible artificial intelligence applications. Attribution methods constitute an important area of explainable deep learning. The attribution problem involves finding parts of the network's input that are the most responsible for the model's output. In this work, we demonstrate that implicit neural representations (INRs) constitute a good framework for generating visual explanations. Firstly, we utilize coordinate-based implicit networks to reformulate and extend the extremal perturbations technique and generate attribution masks. Experimental results confirm the usefulness of our method. For instance, by proper conditioning of the implicit network, we obtain attribution masks that are well-behaved with respect to the imposed area constraints. Secondly, we present an iterative INR-based method that can be used to generate multiple non-overlapping attribution masks for the same image. We depict that a deep learning model may associate the image label with both the appearance of the object of interest as well as with areas and textures usually accompanying the object. Our study demonstrates that implicit networks are well-suited for the generation of attribution masks and can provide interesting insights about the performance of deep learning models.

A major goal of contemporary neuroscience research is to map the structural connectivity of mammalian brain using microscopy imaging data. In this context, the reconstruction of densely labeled axons from two-photon microscopy images is a challenging and important task. The visually overlapping, crossing, and often strongly distorted images of the axons allow many ambiguous interpretations to be made. We address the problem of tracking axons in densely labeled samples of neurons in large image data sets acquired from marmoset brains. Our high-resolution images were acquired using two-photon microscopy and they provided whole brain coverage, occupying terabytes of memory. Both the image distortions and the large data set size frequently make it impractical to apply present-day neuron tracing algorithms to such data due to the optimization of such algorithms to the precise tracing of either single or sparse sets of neurons. Thus, new tracking techniques are needed. We propose a probabilistic axon tracking algorithm (PAT). PAT tackles the tracking of axons in two steps: locally (L-PAT) and globally (G-PAT). L-PAT is a probabilistic tracking algorithm that can tackle distorted, cluttered images of densely labeled axons. L-PAT divides a large micrograph into smaller image stacks. It then processes each image stack independently before mapping the axons in each image to a sparse model of axon trajectories. G-PAT merges the sparse L-PAT models into a single global model of axon trajectories by minimizing a global objective function using a probabilistic optimization method. We demonstrate the superior performance of PAT over standard approaches on synthetic data. Furthermore, we successfully apply PAT to densely labeled axons in large images acquired from marmoset brains.

Tubular shaped networks appear not only in medical images like X-ray-, time-of-flight MRI- or CT-angiograms but also in microscopic images of neuronal networks. We present EMILOVE (Efficient Monte-carlo Image-analysis for the Location Of Vascular Entity), a novel modeling algorithm for tubular networks in biomedical images. The model is constructed using tablet shaped particles and edges connecting them. The particles encode the intrinsic information of tubular structure, including position, scale and orientation. The edges connecting the particles determine the topology of the networks. For simulated data, EMILOVE was able to accurately extract the tubular network. EMILOVE showed high performance in real data as well; it successfully modeled vascular networks in real cerebral X-ray and time-of-flight MRI angiograms. We also show some promising, preliminary results on microscopic images of neurons.

We present a method for densely computing local rotation invariant image descriptors in volumetric images. The descriptors are based on a transformation to the harmonic domain, which we compute very efficiently via differential operators. We show that this fast voxelwise computation is restricted to a family of basis functions that have certain differential relationships. Building upon this finding, we propose local descriptors based on the Gaussian Laguerre and spherical Gabor basis functions and show how the coefficients can be computed efficiently by recursive differentiation. We exemplarily demonstrate the effectiveness of such dense descriptors in a detection and classification task on biological 3D images. In a direct comparison to existing volumetric features, among them 3D SIFT, our descriptors reveal superior performance.

Rotation-invariant descriptions are required in many 3D volumetric image analysis tasks. The histogram-of-oriented-gradient (HOG) is widely used in 2D images and proves to be a very robust local description. This paper concentrates on how to use the HOG feature in 3D volumetric images when rotation-invariance is concerned. This is challenging because of the complexity of 3D rotations. We present a decent solution based on the spherical harmonics theory which is an effective tool for analysing 3D rotations, together with the spherical tensor operations which explore high order tensor information in spherical coordinates. The design is quite general and could be used for different applications. It achieves high scores on Princeton Shape Benchmark and SHREC 2009 Generic Shape Benchmark, and also produces promising results when applying on biological microscopy images.