Atif Khan

Atif Khan, Conor Lawless, Amy Vincent et al.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Atif Khan, Conor Lawless, Amy Vincent et al.

Single cell analysis of skeletal muscle (SM) tissue is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be precise. There is currently no tool or pipeline that makes automatic and precise segmentation and curation of images of SM tissue cross-sections possible. Biomedical scientists in this field rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to get the segmentation right. We believe that automated, precise, reproducible segmentation is possible by training ML models. However, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human tissue sections from healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include $>$ 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibres and annotated reasons for rejecting low quality myofibres and regions in SM tissue images, making this data completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

Nisar Ahmed, H. M. Shahzad Asif, Abdul Rauf Bhatti et al.

Blind image quality assessment is a challenging task particularly due to the unavailability of reference information. Training a deep neural network requires a large amount of training data which is not readily available for image quality. Transfer learning is usually opted to overcome this limitation and different deep architectures are used for this purpose as they learn features differently. After extensive experiments, we have designed a deep architecture containing two CNN architectures as its sub-units. Moreover, a self-collected image database BIQ2021 is proposed with 12,000 images having natural distortions. The self-collected database is subjectively scored and is used for model training and validation. It is demonstrated that synthetic distortion databases cannot provide generalization beyond the distortion types used in the database and they are not ideal candidates for general-purpose image quality assessment. Moreover, a large-scale database of 18.75 million images with synthetic distortions is used to pretrain the model and then retrain it on benchmark databases for evaluation. Experiments are conducted on six benchmark databases three of which are synthetic distortion databases (LIVE, CSIQ and TID2013) and three are natural distortion databases (LIVE Challenge Database, CID2013 and KonIQ-10 k). The proposed approach has provided a Pearson correlation coefficient of 0.8992, 0.8472 and 0.9452 subsequently and Spearman correlation coefficient of 0.8863, 0.8408 and 0.9421. Moreover, the performance is demonstrated using perceptually weighted rank correlation to indicate the perceptual superiority of the proposed approach. Multiple experiments are conducted to validate the generalization performance of the proposed model by training on different subsets of the databases and validating on the test subset of BIQ2021 database.