Dataset Information

I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.

ABSTRACT: The quantification of invasion and migration is an important aspect of cancer research, used both in the study of the molecular processes involved in this collection of diseases and the evaluation of the efficacy of new potential treatments. The transwell assay, while being one of the most widely used techniques for the evaluation of these characteristics, shows a high dependence on the operator's ability to correctly identify the cells and a low protocol standardization. Here we present I-AbACUS, a software tool specifically designed to aid the analysis of transwell assays that automatically and specifically recognizes cells in images of stained membranes and provides the user with a suggested cell count. A complete description of this instrument, together with its validation against the standard analysis technique for this assay is presented. Furthermore, we show that I-AbACUS is versatile and able to elaborate images containing cells with different morphologies and that the obtained results are less dependent on the operator and their experience. We anticipate that this instrument, freely available (Gnu Public Licence GPL v2) at www.marilisacortesi.com as a standalone application, could significantly improve the quantification of invasion and migration of cancer cells.

SUBMITTER: Cortesi M

PROVIDER: S-EPMC5830488 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.

Cortesi Marilisa M Llamosas Estelle E Henry Claire E CE Kumaran Raani-Yogeeta A RA Ng Benedict B Youkhana Janet J Ford Caroline E CE

Scientific reports 20180228 1

The quantification of invasion and migration is an important aspect of cancer research, used both in the study of the molecular processes involved in this collection of diseases and the evaluation of the efficacy of new potential treatments. The transwell assay, while being one of the most widely used techniques for the evaluation of these characteristics, shows a high dependence on the operator's ability to correctly identify the cells and a low protocol standardization. Here we present I-AbACU ...[more]

PMID: 29491372

Similar Datasets

Project description:Given the capacity of Optical Coherence Tomography (OCT) imaging to display structural changes in a wide variety of eye diseases and neurological disorders, the need for OCT image segmentation and the corresponding data interpretation is latterly felt more than ever before. In this paper, we wish to address this need by designing a semi-automatic software program for applying reliable segmentation of 8 different macular layers as well as outlining retinal pathologies such as diabetic macular edema. The software accommodates a novel graph-based semi-automatic method, called "Livelayer" which is designed for straightforward segmentation of retinal layers and fluids. This method is chiefly based on Dijkstra's Shortest Path First (SPF) algorithm and the Live-wire function together with some preprocessing operations on the to-be-segmented images. The software is indeed suitable for obtaining detailed segmentation of layers, exact localization of clear or unclear fluid objects and the ground truth, demanding far less endeavor in comparison to a common manual segmentation method. It is also valuable as a tool for calculating the irregularity index in deformed OCT images. The amount of time (seconds) that Livelayer required for segmentation of Inner Limiting Membrane, Inner Plexiform Layer-Inner Nuclear Layer, Outer Plexiform Layer-Outer Nuclear Layer was much less than that for the manual segmentation, 5 s for the ILM (minimum) and 15.57 s for the OPL-ONL (maximum). The unsigned errors (pixels) between the semi-automatically labeled and gold standard data was on average 2.7, 1.9, 2.1 for ILM, IPL-INL, OPL-ONL, respectively. The Bland-Altman plots indicated perfect concordance between the Livelayer and the manual algorithm and that they could be used interchangeably. The repeatability error was around one pixel for the OPL-ONL and < 1 for the other two. The unsigned errors between the Livelayer and the manual algorithm was 1.33 for ILM and 1.53 for Nerve Fiber Layer-Ganglion Cell Layer in peripapillary B-Scans. The Dice scores for comparing the two algorithms and for obtaining the repeatability on segmentation of fluid objects were at acceptable levels.

Dataset Information

I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.

Publications

I-AbACUS: a Reliable Software Tool for the Semi-Automatic Analysis of Invasion and Migration Transwell Assays.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets