Cluster division is a critical issue in fluorescence microscopy-based analytical cytology when preparation protocols do not provide appropriate separation of objects. Overlooking clustered nuclei and analyzing only isolated nuclei may dramatically increase analysis time or affect the statistical validation of the results. Automatic segmentation of clustered nuclei requires the implementation of specific image segmentation tools. Most algorithms are inspired by one of the two following strategies: 1) cluster division by the detection of internuclei gradients; or 2) division by definition of domains of influence (geometrical approach). Both strategies lead to completely different implementations, and usually algorithms based on a single view strategy fail to correctly segment most clustered nuclei, or perform well just for a specific type of sample. An algorithm based on morphological watersheds has been implemented and tested on the segmentation of microscopic nuclei clusters. This algorithm provides a tool that can be used for the implementation of both gradient- and domain-based algorithms, and, more importantly, for the implementation of mixed (gradient- and shape-based) algorithms. Using this algorithm, almost 90% of the test clusters were correctly segmented in peripheral blood and bone marrow preparations. The algorithm was valid for both types of samples, using the appropriate markers and transformations. Cytometry 28:289–297, 1997.

Zebrafish Development in 3D: Vertebrate development has classically been characterized qualitatively, but—by combining expertise in physics, mathematics, and biology— Olivier et al. (p. 967 ) used label-free conformal nonlinear time-lapse microscopy and image analysis to calculate the spatiotemporal cell lineage of zebrafish embryos throughout their first 10 division cycles. The work reconstructs complete lineage trees, annotated with cell-shape measurements, and allows for visualization with interactive tools.

This work describes a systematic evaluation of several autofocus functions used for analytical fluorescent image cytometry studies of counterstained nuclei. Focusing is the first step in the automatic fluorescence in situ hybridization analysis of cells. Thirteen functions have been evaluated using qualitative and quantitative procedures. For the last of these procedures a figure‐of‐merit (FOM) is defined and proposed. This new FOM takes into account five important features of the focusing function. Our results show that functions based on correlation measures have the best performance for this type of image.

We propose a new spatio-temporal elastic registration algorithm for motion reconstruction from a series of images. The specific application is to estimate displacement fields from two-dimensional ultrasound sequences of the heart. The basic idea is to find a spatio-temporal deformation field that effectively compensates for the motion by minimizing a difference with respect to a reference frame. The key feature of our method is the use of a semi-local spatio-temporal parametric model for the deformation using splines, and the reformulation of the registration task as a global optimization problem. The scale of the spline model controls the smoothness of the displacement field. Our algorithm uses a multiresolution optimization strategy to obtain a higher speed and robustness. We evaluated the accuracy of our algorithm using a synthetic sequence generated with an ultrasound simulation package, together with a realistic cardiac motion model. We compared our new global multiframe approach with a previous method based on pairwise registration of consecutive frames to demonstrate the benefits of introducing temporal consistency. Finally, we applied the algorithm to the regional analysis of the left ventricle. Displacement and strain parameters were evaluated showing significant differences between the normal and pathological segments, thereby illustrating the clinical applicability of our method.

Respiratory motion in emission tomography leads to reduced image quality. Developed correction methodology has been concentrating on the use of respiratory synchronized acquisitions leading to gated frames. Such frames, however, are of low signal-to-noise ratio as a result of containing reduced statistics. In this work, we describe the implementation of an elastic transformation within a list-mode-based reconstruction for the correction of respiratory motion over the thorax, allowing the use of all data available throughout a respiratory motion average acquisition. The developed algorithm was evaluated using datasets of the NCAT phantom generated at different points throughout the respiratory cycle. List-mode-data-based PET-simulated frames were subsequently produced by combining the NCAT datasets with Monte Carlo simulation. A non-rigid registration algorithm based on B-spline basis functions was employed to derive transformation parameters accounting for the respiratory motion using the NCAT dynamic CT images. The displacement matrices derived were subsequently applied during the image reconstruction of the original emission list mode data. Two different implementations for the incorporation of the elastic transformations within the one-pass list mode EM (OPL-EM) algorithm were developed and evaluated. The corrected images were compared with those produced using an affine transformation of list mode data prior to reconstruction, as well as with uncorrected respiratory motion average images. Results demonstrate that although both correction techniques considered lead to significant improvements in accounting for respiratory motion artefacts in the lung fields, the elastic-transformation-based correction leads to a more uniform improvement across the lungs for different lesion sizes and locations.

Glaucoma detection in color fundus images is a challenging task that requires expertise and years of practice. In this study we exploited the application of different Convolutional Neural Networks (CNN) schemes to show the influence in the performance of relevant factors like the data set size, the architecture and the use of transfer learning vs newly defined architectures. We also compared the performance of the CNN based system with respect to human evaluators and explored the influence of the integration of images and data collected from the clinical history of the patients. We accomplished the best performance using a transfer learning scheme with VGG19 achieving an AUC of 0.94 with sensitivity and specificity ratios similar to the expert evaluators of the study. The experimental results using three different data sets with 2313 images indicate that this solution can be a valuable option for the design of a computer aid system for the detection of glaucoma in large-scale screening programs.