CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.

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CellProfiler 3.0: Next-generation image processing for biology.

Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.

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Objective comparison of particle tracking methods

Objective To observe the effect of intensive insulin therapy on the critically ill patients with stress hyperglycemia in ICU.Methods One hundred and ten critically ill patients in ICU were randomly divided into two groups,the intensive insulin therapy group(n=55) and control group(n=55).The blood glucose in the intensive insulin therapy group was controlled at 4.4 to 6.1 mmol/L,and the blood glucose in control group was controlled at 10.0 to 11.1 mmol/L.The two groups were observed and compared the days in the ICU,the numbers of patients requiring mechanical ventilation,the days of mechanical ventilation,the incidences of infection in hospital,the days of using antibiotics,Acute Physiology and Chronic Health Evaluation Ⅱ score of the last day in ICU,the morbidity of multiple organ failure,the morbidity of hypoglycemia and mortality.Results All the above indices except morbidity of hypoglycemia were significantly lower in the intensive insulin therapy group than those in control group(P0.05 or P0.01).Conclusion Intensive insulin therapy and keeping blood glucose at 4.4 to 6.1 mmol/L can improve the clinical curative effect and reduce the mortality for the critically ill patients with stress hyperglycemia,

Intensive insulin therapy for the critically ill patients with stress hyperglycemia

The endoplasmic reticulum (ER) is a membranous intracellular organelle and the first compartment of the secretory pathway As such, the ER contributes to the production and folding of approximately one-third of cellular proteins, and is thus inextricably linked to the maintenance of cellular homeostasis and the fine balance between health and disease Specific ER stress signalling pathways, collectively known as the unfolded protein response (UPR), are required for maintaining ER homeostasis The UPR is triggered when ER protein folding capacity is overwhelmed by cellular demand and the UPR initially aims to restore ER homeostasis and normal cellular functions However, if this fails, then the UPR triggers cell death In this review, we provide a UPR signalling-centric view of ER functions, from the ER's discovery to the latest advancements in the understanding of ER and UPR biology Our review provides a synthesis of intracellular ER signalling revolving around proteostasis and the UPR, its impact on other organelles and cellular behaviour, its multifaceted and dynamic response to stress and its role in physiology, before finally exploring the potential exploitation of this knowledge to tackle unresolved biological questions and address unmet biomedical needs Thus, we provide an integrated and global view of existing literature on ER signalling pathways and their use for therapeutic purposes

/pdf/endoplasmic-reticulum-stress-signalling-from-basic-1ncpnvizt7.pdf

Endoplasmic Reticulum Stress signalling - from basic mechanisms to clinical applications

Motivation: Automatic tracking of cells in multidimensional time� lapse fluorescence microscopy is an important task in many biomed� ical applications. A novel framework for objective evaluation of cell tracking algorithms has been established under the auspices of the IEEE International Symposium on Biomedical Imaging 2013 Cell Tracking Challenge. In this paper, we present the logistics, datasets, methods and results of the challenge and lay down the principles for future uses of this benchmark. Results: The main contributions of the challenge include the crea� tion of a comprehensive video dataset repository and the definition of objective measures for comparison and ranking of the algorithms. With this benchmark, six algorithms covering a variety of segmenta� tion and tracking paradigms have been compared and ranked based on their performance on both synthetic and real datasets. Given the diversity of the datasets, we do not declare a single winner of the challenge. Instead, we present and discuss the results for each individual dataset separately. Availability and implementation: The challenge website (http://www.codesolorzano.com/celltrackingchallenge) provides access to the training and competition datasets, along with the ground truth of the training videos. It also provides access to Win� dows and Linux executable files of the evaluation software and most of the algorithms that competed in the challenge.

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A benchmark for comparison of cell tracking algorithms

Image cytometry still faces the problem of the quality of cell
image analysis results. Degradations caused by cell
preparation, optics and electronics considerably affect most 2D
and 3D cell image data acquired using optical microscopy. That
is why image processing algorithms applied to these data
typically offer imprecise and unreliable results. We have
created a toolbox that can generate 3D digital phantoms of
specific cellular components along with their corresponding
images degraded by specific optics and electronics. The user
can then apply image analysis methods to such simulated image
data. The analysis results can be compared with ground truth
derived from input object digital phantoms. In this way, image
analysis methods can be compared to each other and their
quality can be computed. We have also evaluated the
plausibility of the synthetic images, measured by their
similarity to real image data.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/cyto.a.20714

Generation of digital phantoms of cell nuclei and simulation of image formation in 3D image cytometry.

Human induced pluripotent stem cells (hiPSCs) play roles in both disease modelling and regenerative medicine. It is critical that the genomic integrity of the cells remains intact and that the DNA repair systems are fully functional. In this article, we focused on the detection of DNA double-strand breaks (DSBs) by phosphorylated histone H2AX (known as γH2AX) and p53-binding protein 1 (53BP1) in three distinct lines of hiPSCs, their source cells, and one line of human embryonic stem cells (hESCs). We measured spontaneously occurring DSBs throughout the process of fibroblast reprogramming and during long-term in vitro culturing. To assess the variations in the functionality of the DNA repair system among the samples, the number of DSBs induced by γ-irradiation and the decrease over time was analysed. The foci number was detected by fluorescence microscopy separately for the G1 and S/G2 cell cycle phases. We demonstrated that fibroblasts contained a low number of non-replication-related DSBs, while this number increased after reprogramming into hiPSCs and then decreased again after long-term in vitro passaging. The artificial induction of DSBs revealed that the repair mechanisms function well in the source cells and hiPSCs at low passages, but fail to recognize a substantial proportion of DSBs at high passages. Our observations suggest that cellular reprogramming increases the DSB number but that the repair mechanism functions well. However, after prolonged in vitro culturing of hiPSCs, the repair capacity decreases.

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DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing.

The role of the endoplasmic reticulum stress in stemness, pluripotency and development

In this study, the effects of insulin and dexamethasone on the
expression and mRNA transcription of 4 pulmonary
surfactant-associated proteins [surfactant protein (SFTP)A,
SFTPB, SFTPC and SFTPD] were examined. The commercially
available cell lines, A549 and H441, were used as acceptable
models of lung surfactant-producing cells. Subsequently, the
effects of insulin on the expression of surfactant-associated
proteins were examined in patients with lung adenocarcinoma
during lung resection. Our results demonstrated the inhibitory
effects of insulin on the transcription of the SFTPB, SFTPC and
SFTPD genes in H441 cells and the SFTPB gene in A549 cells.
Treatment with insulin significantly decreased the protein
expression of SFTPA1 and SFTPA2 in the H441 cells and that of
proSFTPB in the A549 cells. Dexamethasone promoted the
transcription of the SFTPB, SFTPC and SFTPD genes in the A549
and H441 cells and reduced the transcription of the SFTPA1 and
SFTPA2 genes in the H441 cells (SFTPA mRNA expression was not
detected in A549 cells). Furthermore, we demonstrated that the
mRNA levels of the selected genes were significantly lower in
the cell lines compared to the lung tissue. A549 and H441 cells
represent similar cell types. Yet, in our experiments, these
cells reacted differently to insulin and/or dexamethasone
treatment, and the mRNA levels of their main protein products,
surfactant-associated proteins,were significantly lower than
those in real tissue. Therefore, the results obtained in this
study challenge the suitability of A549 and H441 cells as
models of type II pneumocytes and Clara cells, respectively.
However, we successfully demonstrate the possibility of
studying the effects of insulin on pulmonary
surfactant-associated genes and proteins in patients with lung
adenocarcinoma.

/pdf/differential-effects-of-insulin-and-dexamethasone-on-4jfpnm8wqm.pdf

Differential effects of insulin and dexamethasone on pulmonary surfactant-associated genes and proteins in A549 and H441 cells and lung tissue.

In recent years many various biomedical image segmentation methods have appeared. Though typically presented to be successful the majority of them was not properly tested against ground truth images. The obvious way of testing the quality of new segmentation was based on visual inspection by a specialist in the given field. The novel 3D biomedical image data simulator is presented in this paper. It offers the results of high quality. The comparison of generated synthetic data is compared against real image data using standard similarity techniques.

Stanislav Stejskal

Papers

Generation of digital phantoms of cell nuclei and simulation of image formation in 3D image cytometry.

DNA double-strand breaks in human induced pluripotent stem cell reprogramming and long-term in vitro culturing.

The role of the endoplasmic reticulum stress in stemness, pluripotency and development

Differential effects of insulin and dexamethasone on pulmonary surfactant-associated genes and proteins in A549 and H441 cells and lung tissue.

On simulating 3D fluorescent microscope images