Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets.

Recent advances in computer vision have led to significant progress in the generation of realistic image data, with denoising diffusion probabilistic models proving to be a particularly effective method. In this study, we demonstrate that diffusion models can effectively generate fully-annotated microscopy image data sets through an unsupervised and intuitive approach, using rough sketches of desired structures as the starting point. The proposed pipeline helps to reduce the reliance on manual annotations when training deep learning-based segmentation approaches and enables the segmentation of diverse datasets without the need for human annotations. We demonstrate that segmentation models trained with a small set of synthetic image data reach accuracy levels comparable to those of generalist models trained with a large and diverse collection of manually annotated image data, thereby offering a streamlined and specialized application of segmentation models.

Definition and Quantification of Three-Dimensional Imaging Targets to Phenotype Pre-Eclampsia Subtypes: An Exploratory Study.

Pre-eclampsia is a severe placenta-related complication of pregnancy with limited early diagnostic and therapeutic options. Aetiological knowledge is controversial, and there is no universal consensus on what constitutes the early and late phenotypes of pre-eclampsia. Phenotyping of native placental three-dimensional (3D) morphology offers a novel approach to improve our understanding of the structural placental abnormalities in pre-eclampsia. Healthy and pre-eclamptic placental tissues were imaged with multiphoton microscopy (MPM). Imaging based on inherent signal (collagen, and cytoplasm) and fluorescent staining (nuclei, and blood vessels) enabled the visualization of placental villous tissue with subcellular resolution. Images were analysed with a combination of open source (FIJI, VMTK, Stardist, MATLAB, DBSCAN), and commercially (MATLAB) available software. Trophoblast organization, 3D-villous tree structure, syncytial knots, fibrosis, and 3D-vascular networks were identified as quantifiable imaging targets. Preliminary data indicate increased syncytial knot density with characteristic elongated shape, higher occurrence of paddle-like villous sprouts, abnormal villous volume-to-surface ratio, and decreased vascular density in pre-eclampsia compared to control placentas. The preliminary data presented indicate the potential of quantifying 3D microscopic images for identifying different morphological features and phenotyping pre-eclampsia in placental villous tissue.

Using positional information to provide context for biological image analysis with MorphoGraphX 2.0.

Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here, we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015⁠) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.

3D fluorescence microscopy data synthesis for segmentation and benchmarking.

Automated image processing approaches are indispensable for many biomedical experiments and help to cope with the increasing amount of microscopy image data in a fast and reproducible way. Especially state-of-the-art deep learning-based approaches most often require large amounts of annotated training data to produce accurate and generalist outputs, but they are often compromised by the general lack of those annotated data sets. In this work, we propose how conditional generative adversarial networks can be utilized to generate realistic image data for 3D fluorescence microscopy from annotation masks of 3D cellular structures. In combination with mask simulation approaches, we demonstrate the generation of fully-annotated 3D microscopy data sets that we make publicly available for training or benchmarking. An additional positional conditioning of the cellular structures enables the reconstruction of position-dependent intensity characteristics and allows to generate image data of different quality levels. A patch-wise working principle and a subsequent full-size reassemble strategy is used to generate image data of arbitrary size and different organisms. We present this as a proof-of-concept for the automated generation of fully-annotated training data sets requiring only a minimum of manual interaction to alleviate the need of manual annotations.

Segmenting renal whole slide images virtually without training data.

Digital pathology is a field of increasing interest and requires automated systems for processing huge amounts of digital data. The development of supervised-learning based automated systems is aggravated by the fact that image properties can change from slide to slide. In this work, the focus is on the segmentation of the glomeruli constituting the most important regions-of-interest in renal histopathology. We propose and investigate a two-stage pipeline consisting of a weakly supervised patch-based detection and a precise segmentation. The proposed methods do not need any previously obtained training data. For adapting and optimizing this model, a kernel two-sample test is applied. For the segmentation stage, unsupervised segmentation methods including level-set and polygon-fitting approaches are adapted, combined and evaluated. Overall, with the best performing polygon-fitting segmentation method, 51% of glomeruli were segmented with sufficient accuracy (DSC > 0.8). 42% of the detections were false positives. Due to the difficult application scenario in combination with the small required training corpus, the obtained performance is assessed as good. Strategies for increasing the segmentation performance even further are discussed in detail.