Generative modeling of living cells with SO(3)-equivariant implicit neural representations

Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to improve these methods. This requires the synthesis of cell shapes as well as corresponding microscopy images using generative models. To synthesize realistic living cell shapes, the shape representation used by the generative model should be able to accurately represent fine details and changes in topology, which are common in cells. These requirements are not met by 3D voxel masks, which are restricted in resolution, and polygon meshes, which do not easily model processes like cell growth and mitosis. In this work, we propose to represent living cell shapes as level sets of signed distance functions (SDFs) which are estimated by neural networks. We optimize a fully-connected neural network to provide an implicit representation of the SDF value at any point in a 3D+time domain, conditioned on a learned latent code that is disentangled from the rotation of the cell shape. We demonstrate the effectiveness of this approach on cells that exhibit rapid deformations (Platynereis dumerilii), cells that grow and divide (C. elegans), and cells that have growing and branching filopodial protrusions (A549 human lung carcinoma cells). A quantitative evaluation using shape features, Hausdorff distance, and Dice similarity coefficients of real and synthetic cell shapes shows that our model can generate topologically plausible complex cell shapes in 3D+time with high similarity to real living cell shapes. Finally, we show how microscopy images of living cells that correspond to our generated cell shapes can be synthesized using an image-to-image model.Comment: Medical Image Analysis 2023 (Submitted

H-NeXt: The next step towards roto-translation invariant networks

The widespread popularity of equivariant networks underscores the significance of parameter efficient models and effective use of training data. At a time when robustness to unseen deformations is becoming increasingly important, we present H-NeXt, which bridges the gap between equivariance and invariance. H-NeXt is a parameter-efficient roto-translation invariant network that is trained without a single augmented image in the training set. Our network comprises three components: an equivariant backbone for learning roto-translation independent features, an invariant pooling layer for discarding roto-translation information, and a classification layer. H-NeXt outperforms the state of the art in classification on unaugmented training sets and augmented test sets of MNIST and CIFAR-10.Comment: Appears in British Machine Vision Conference 2023 (BMVC 2023

Augmented Equivariant Attention Networks for Microscopy Image Reconstruction

It is time-consuming and expensive to take high-quality or high-resolution electron microscopy (EM) and fluorescence microscopy (FM) images. Taking these images could be even invasive to samples and may damage certain subtleties in the samples after long or intense exposures, often necessary for achieving high-quality or high resolution in the first place. Advances in deep learning enable us to perform image-to-image transformation tasks for various types of microscopy image reconstruction, computationally producing high-quality images from the physically acquired low-quality ones. When training image-to-image transformation models on pairs of experimentally acquired microscopy images, prior models suffer from performance loss due to their inability to capture inter-image dependencies and common features shared among images. Existing methods that take advantage of shared features in image classification tasks cannot be properly applied to image reconstruction tasks because they fail to preserve the equivariance property under spatial permutations, something essential in image-to-image transformation. To address these limitations, we propose the augmented equivariant attention networks (AEANets) with better capability to capture inter-image dependencies, while preserving the equivariance property. The proposed AEANets captures inter-image dependencies and shared features via two augmentations on the attention mechanism, which are the shared references and the batch-aware attention during training. We theoretically derive the equivariance property of the proposed augmented attention model and experimentally demonstrate its consistent superiority in both quantitative and visual results over the baseline methods.Comment: 11 pages, 8 figure

Roto-Translation Equivariant Convolutional Networks: Application to Histopathology Image Analysis

Rotation-invariance is a desired property of machine-learning models for medical image analysis and in particular for computational pathology applications. We propose a framework to encode the geometric structure of the special Euclidean motion group SE(2) in convolutional networks to yield translation and rotation equivariance via the introduction of SE(2)-group convolution layers. This structure enables models to learn feature representations with a discretized orientation dimension that guarantees that their outputs are invariant under a discrete set of rotations. Conventional approaches for rotation invariance rely mostly on data augmentation, but this does not guarantee the robustness of the output when the input is rotated. At that, trained conventional CNNs may require test-time rotation augmentation to reach their full capability. This study is focused on histopathology image analysis applications for which it is desirable that the arbitrary global orientation information of the imaged tissues is not captured by the machine learning models. The proposed framework is evaluated on three different histopathology image analysis tasks (mitosis detection, nuclei segmentation and tumor classification). We present a comparative analysis for each problem and show that consistent increase of performances can be achieved when using the proposed framework

Efficient Brain Tumor Segmentation with Multiscale Two-Pathway-Group Conventional Neural Networks

© 2013 IEEE. Manual segmentation of the brain tumors for cancer diagnosis from MRI images is a difficult, tedious, and time-consuming task. The accuracy and the robustness of brain tumor segmentation, therefore, are crucial for the diagnosis, treatment planning, and treatment outcome evaluation. Mostly, the automatic brain tumor segmentation methods use hand designed features. Similarly, traditional methods of deep learning such as convolutional neural networks require a large amount of annotated data to learn from, which is often difficult to obtain in the medical domain. Here, we describe a new model two-pathway-group CNN architecture for brain tumor segmentation, which exploits local features and global contextual features simultaneously. This model enforces equivariance in the two-pathway CNN model to reduce instabilities and overfitting parameter sharing. Finally, we embed the cascade architecture into two-pathway-group CNN in which the output of a basic CNN is treated as an additional source and concatenated at the last layer. Validation of the model on BRATS2013 and BRATS2015 data sets revealed that embedding of a group CNN into a two pathway architecture improved the overall performance over the currently published state-of-the-art while computational complexity remains attractive