A new Image Segmentation Algorithm with Applications in Confocal Microscopy Analysis

Abstract

Gene regulatory networks (GRNs) represent the molecular interactions that govern the behavior of cells in tissues during development. The building and analysis of GRNs require quantitative information on gene expression from tissues. Laser Scanning Confocal Microscopy (LSCM) is commonly used to obtain such information, where immunofluorescence signal can be used as a correlate of gene expression or protein levels. However, a critical step for the extraction of this information is the segmentation of LSCM digital images. Popular segmentation algorithms are frequently based on watershed methods. Here we present an algorithm for the 3D segmentation of nuclei from LSCM (x,y,z) image stacks based on regional merging and graph contractions. This algorithm outperforms watershed methods, especially when the density of images along the z-axis is low and there is a high nuclear signal crowding. In addition, it reduces the parameterization since no filter is needed in order to prevent signal noise side effects (e.g. oversegmentation). Based on this algorithm, we developed an application (iFLIC, immunoFLuorescence Imaging Cytometry tool) for the Java Virtual Machine (JVM). The application supports basic operations for reading, writing and filtering 8-bit depth multicolor TIFF image formats, including indexed file directories (IFD), which are provided by the Java Advanced Imaging (JAI) library. It also provides with basic 3D rendering and ROI specification that make extensive use of the Java3D library. iFLIC is also a plugin based application powered by the Java Plugin Platform (JPF), so each specific operation is declared as a unique command associated to one plugin and linked to a common interface. Results from segmentation can be exported both as TIFF images and a descriptive file format (iFLIC format).

La fraseología en las columnas sobre la lengua (CSL): objeto temático y expresión de un imaginario lingüístico

“…En nada mejora conducir una orquesta a dirigirla; carece de sentido pues, mudar de lengua para decir lo mismo. (Lázaro Carreter 1997: 483) Atendiendo a la clasificación establecida de las ufs, un buen número de columnas están dedicadas a expresiones de carácter gramatical como locuciones prepositivas y locuciones conjuntivas, formadas por partículas vacías de significado a las que Casares llamó locuciones conexivas (Casares Sánchez 1992[1950: 171). En el periodo cronológico revisado, Cavia se preocupa por este tipo de unidades y plantea que ciertas locuciones formadas por dos palabras (a pesar y a propósito) se puedan escribir como una sola, pese a ir en contra de la autoridad académica.…”

A Toggle-Switch and a Feed-Forward Loop Engage in the Control of the Drosophila Retinal Determination Gene Network

“…Centroids were projected onto the closer position of this surface and their trajectories within (up to the TRF origin) computed for both the x and y directions, replacing the original coordinates. The full description of iFLIC, the image segmentation software, can be found in Sanchez-Aragon and Casares (2019).…”

“…The confocal data used in this study included the nuclear marker DAPI. Nuclei are segmented in 3D using iFLIC, a custom made software (Sanchez-Aragon and Casares, 2019) of the RDGN using coupled differential equations. The model equations were built as follows:…”

“…As a first step, we used an image analysis pipeline, based on watershed, to segment nuclei in 3D, using DAPI as nuclear marker, and recording the information on the position of the centroid of each nucleus. Next, each nucleus is assigned gene expression values as fluorescence intensity (Figure 1) (Naval-Sanchez et al, 2013;Sanchez-Aragon and Casares, 2019). Although the eye primordium (or "eye disc") is an epithelial monolayer, it becomes folded as development proceeds.…”