Dataset Information

Computer-assisted counting of retinal cells by automatic segmentation after TV denoising.

ABSTRACT:

Background

Quantitative evaluation of mosaics of photoreceptors and neurons is essential in studies on development, aging and degeneration of the retina. Manual counting of samples is a time consuming procedure while attempts to automatization are subject to various restrictions from biological and preparation variability leading to both over- and underestimation of cell numbers. Here we present an adaptive algorithm to overcome many of these problems.Digital micrographs were obtained from cone photoreceptor mosaics visualized by anti-opsin immuno-cytochemistry in retinal wholemounts from a variety of mammalian species including primates. Segmentation of photoreceptors (from background, debris, blood vessels, other cell types) was performed by a procedure based on Rudin-Osher-Fatemi total variation (TV) denoising. Once 3 parameters are manually adjusted based on a sample, similarly structured images can be batch processed. The module is implemented in MATLAB and fully documented online.

Results

The object recognition procedure was tested on samples with a typical range of signal and background variations. We obtained results with error ratios of less than 10% in 16 of 18 samples and a mean error of less than 6% compared to manual counts.

Conclusions

The presented method provides a traceable module for automated acquisition of retinal cell density data. Remaining errors, including addition of background items, splitting or merging of objects might be further reduced by introduction of additional parameters. The module may be integrated into extended environments with features such as 3D-acquisition and recognition.

SUBMITTER: Bredies K

PROVIDER: S-EPMC3835550 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Computer-assisted counting of retinal cells by automatic segmentation after TV denoising.

Bredies Kristian K Wagner Marcus M Schubert Christian C Ahnelt Peter P

BMC ophthalmology 20131020

<h4>Background</h4>Quantitative evaluation of mosaics of photoreceptors and neurons is essential in studies on development, aging and degeneration of the retina. Manual counting of samples is a time consuming procedure while attempts to automatization are subject to various restrictions from biological and preparation variability leading to both over- and underestimation of cell numbers. Here we present an adaptive algorithm to overcome many of these problems.Digital micrographs were obtained fr ...[more]

PMID: 24138794

Similar Datasets

Project description:IntroductionBoth Hip Dysplasia(DDH) and Femoro-acetabular-Impingement(FAI) are complex three-dimensional hip pathologies causing hip pain and osteoarthritis in young patients. 3D-MRI-based models were used for radiation-free computer-assisted surgical planning. Automatic segmentation of MRI-based 3D-models are preferred because manual segmentation is time-consuming.To investigate(1) the difference and(2) the correlation for femoral head coverage(FHC) between automatic MR-based and manual CT-based 3D-models and (3) feasibility of preoperative planning in symptomatic patients with hip diseases.MethodsWe performed an IRB-approved comparative, retrospective study of 31 hips(26 symptomatic patients with hip dysplasia or FAI). 3D MRI sequences and CT scans of the hip were acquired. Preoperative MRI included axial-oblique T1 VIBE sequence(0.8 mm3 isovoxel) of the hip joint. Manual segmentation of MRI and CT scans were performed. Automatic segmentation of MRI-based 3D-models was performed using deep learning.Results(1)The difference between automatic and manual segmentation of MRI-based 3D hip joint models was below 1 mm(proximal femur 0.2 ± 0.1 mm and acetabulum 0.3 ± 0.5 mm). Dice coefficients of the proximal femur and the acetabulum were 98 % and 97 %, respectively. (2)The correlation for total FHC was excellent and significant(r = 0.975, p < 0.001) between automatic MRI-based and manual CT-based 3D-models. Correlation for total FHC (r = 0.979, p < 0.001) between automatic and manual MR-based 3D models was excellent.(3)Preoperative planning and simulation of periacetabular osteotomy was feasible in all patients(100 %) with hip dysplasia or acetabular retroversion.ConclusionsAutomatic segmentation of MRI-based 3D-models using deep learning is as accurate as CT-based 3D-models for patients with hip diseases of childbearing age. This allows radiation-free and patient-specific preoperative simulation and surgical planning of periacetabular osteotomy for patients with DDH.

Dataset Information

Computer-assisted counting of retinal cells by automatic segmentation after TV denoising.

Background

Results

Conclusions

Publications

Computer-assisted counting of retinal cells by automatic segmentation after TV denoising.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets