Cell counting tool parameters optimization approach for electroporation efficiency determination of attached cells in phase contrast images

Co-assembling bioactive short peptide nanofibers coated silk scaffolds induce neurite outgrowth of PC12 cells

Controlling biomolecular-cell interactions is crucial for the design of scaffolds for tissue engineering (TE). Regenerated silk fibroin (RSF) has been extensively used as TE scaffolds, however, RSF showed poor attachment of neuronal cells, such as rat pheochromocytoma (PC12) cells. In this work, amphiphilic peptides containing a hydrophobic isoleucine tail (I3) and laminin or fibronectin derived peptides (IKVAV, PDSGR, YIGSR, RGDS and PHSRN) were designed for promoting scaffold-cell interaction. Three of them (I3KVAV, I3RGDS and I3YIGSR) can self-assemble into nanofibers, therefore, were used to enhance the application of RSF in neuron TE. Live / dead assays revealed that the peptides exhibited negligible cytotoxicity against PC12 cells. The specific interaction between PC12 cells and the peptides were investigate using atomic force microscopy (AFM). The results indicated a synergistic effect in the designed peptides, promoting cellular attachment, proliferation and morphology changes. In addition, AFM results showed that co-assembling peptides I3KVAV and I3YIGSR possesses the best regulation of proliferation and attachment of PC12 cells, consistent with immunofluorescence staining results. Moreover, cell culture with hydrogels revealed that a mixture of peptides I3KVAV and I3YIGSR can also promote 3D neurites outgrowth. The approach of combining two different self-assembling peptides shows great potential for nerve regeneration applications.

Aminosilane Functionalized Aligned Fiber PCL Scaffolds for Peripheral Nerve Repair

Silane modification is a simple and cost-effective tool to modify existing biomaterials for tissue engineering applications. Aminosilane layer deposition has previously been shown to control NG108-15 neuronal cell and primary Schwann cell adhesion and differentiation by controlling deposition of ─NH2 groups at the submicron scale across the entirety of a surface by varying silane chain length. This is the first study toreport depositing 11-aminoundecyltriethoxysilane (CL11) onto aligned Polycaprolactone (PCL) scaffolds for peripheral nerve regeneration. Fibers are manufactured via electrospinning and characterized using water contact angle measurements, atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). Confirmed modified fibers are investigated using in vitro cell culture of NG108-15 neuronal cells and primary Schwann cells to determine cell viability, cell differentiation, and phenotype. CL11-modified fibers significantly support NG108-15 neuronal cell and Schwann cell viability. NG108-15 neuronal cell differentiation maintains Schwann cell phenotype compared to unmodified PCL fiber scaffolds. 3D ex vivo culture of Dorsal root ganglion explants (DRGs) confirms further Schwann cell migration and longer neurite outgrowth from DRG explants cultured on CL11 fiber scaffolds compared to unmodified scaffolds. Thus, a reproducible and cost-effective tool is reported to modify biomaterials with functional amine groups that can significantly improve nerve guidance devices and enhance nerve regeneration.

Densely Convolutional Spatial Attention Network for nuclei segmentation of histological images for computational pathology

Introduction

Automatic nuclear segmentation in digital microscopic tissue images can aid pathologists to extract high-quality features for nuclear morphometrics and other analyses. However, image segmentation is a challenging task in medical image processing and analysis. This study aimed to develop a deep learning-based method for nuclei segmentation of histological images for computational pathology.

Methods

The original U-Net model sometime has a caveat in exploring significant features. Herein, we present the Densely Convolutional Spatial Attention Network (DCSA-Net) model based on U-Net to perform the segmentation task. Furthermore, the developed model was tested on external multi-tissue dataset - MoNuSeg. To develop deep learning algorithms for well-segmenting nuclei, a large quantity of data are mandatory, which is expensive and less feasible. We collected hematoxylin and eosin-stained image data sets from two hospitals to train the model with a variety of nuclear appearances. Because of the limited number of annotated pathology images, we introduced a small publicly accessible data set of prostate cancer (PCa) with more than 16,000 labeled nuclei. Nevertheless, to construct our proposed model, we developed the DCSA module, an attention mechanism for capturing useful information from raw images. We also used several other artificial intelligence-based segmentation methods and tools to compare their results to our proposed technique.

Results

To prioritize the performance of nuclei segmentation, we evaluated the model's outputs based on the Accuracy, Dice coefficient (DC), and Jaccard coefficient (JC) scores. The proposed technique outperformed the other methods and achieved superior nuclei segmentation with accuracy, DC, and JC of 96.4% (95% confidence interval [CI]: 96.2 - 96.6), 81.8 (95% CI: 80.8 - 83.0), and 69.3 (95% CI: 68.2 - 70.0), respectively, on the internal test data set.

Conclusion

Our proposed method demonstrates superior performance in segmenting cell nuclei of histological images from internal and external datasets, and outperforms many standard segmentation algorithms used for comparative analysis.

Aligned Polyhydroxyalkanoate Blend Electrospun Fibers as Intraluminal Guidance Scaffolds for Peripheral Nerve Repair

The use of nerve guidance conduits (NGCs) to treat peripheral nerve injuries is a favorable approach to the current "gold standard" of autografting. However, as simple hollow tubes, they lack specific topographical and mechanical guidance cues present in nerve grafts and therefore are not suitable for treating large gap injuries (30-50 mm). The incorporation of intraluminal guidance scaffolds, such as aligned fibers, has been shown to increase neuronal cell neurite outgrowth and Schwann cell migration distances. A novel blend of PHAs, P(3HO)/P(3HB) (50:50), was investigated for its potential as an intraluminal aligned fiber guidance scaffold. Aligned fibers of 5 and 8 μm diameter were manufactured by electrospinning and characterized using SEM. Fibers were investigated for their effect on neuronal cell differentiation, Schwann cell phenotype, and cell viability in vitro. Overall, P(3HO)/P(3HB) (50:50) fibers supported higher neuronal and Schwann cell adhesion compared to PCL fibers. The 5 μm PHA blend fibers also supported significantly higher DRG neurite outgrowth and Schwann cell migration distance using a 3D ex vivo nerve injury model.

Automatic cell counting for phase-contrast microscopic images based on a combination of Otsu and watershed segmentation method

Cell counting plays a vital role in biomedical researches. However, manual cell counting is time-consuming, laborious, and low efficiency and has a high counting error rate problem. An automatic counting approach for Hela cells of phase-contrast microscopic images is proposed based on the combination of Otsu and watershed segmentation methods to solve the mentioned issues. Firstly, image preprocessing is performed. Secondly, the Otsu method was used to obtain an automatic global optimal threshold for segmentation to achieve batch counting of images. Thirdly, the marker watershed was performed to separate adherent cells and to avoid over-segmentation simultaneously. Finally, cells in phase-contrast microscopic images were counted by detecting the numbers of connected domains in the binary image. Taking the manual counting result as the counting standard and MIS, INC, and ACC are used as evaluation indicators. The experimental results showed that the average values of MIS, INC, and ACC of the proposed method are only 3.31%, 3.49%, and 96.69%, respectively. Additionally, each cell image was counted only takes 0.65 s on averagely. To further test the performance of the proposed method, a comparative experiment was carried out by Image J, and the result shows that the proposed method has a better counting performance with a higher average accuracy of 96.55% to Image J with 93.39%.The proposed method for cell counting is simple, feasible, fast and high accurate, and it can be used as an effective method for cell counting of the phase-contrast microscopic images.

Continuous monitoring of cell transfection efficiency with micropatterned substrates

The effect of cell-cell contact on gene transfection is mainly unknown. Usually, transfection is carried out in batch cell cultures without control over cellular interactions, and efficiency analysis relies on complex and expensive protocols commonly involving flow cytometry as the final analytical step. Novel platforms and cell patterning are being studied to control cellular interactions and improve quantification methods. In this study, we report the use of surface patterning of fibronectin for the generation of two types of mesenchymal stromal cell patterns: single-cell patterns without cell-to-cell contact, and small cell-colony patterns. Both scenarios allowed the integration of the full transfection process and the continuous monitoring of thousands of individualized events by fluorescence microscopy. Our results showed that cell-to-cell contact clearly affected the transfection, as single cells presented a maximum transfection peak 6 h earlier and had a 10% higher transfection efficiency than cells with cell-to-cell contact.

Cost effective optimised synthetic surface modification strategies for enhanced control of neuronal cell differentiation and supporting neuronal and Schwann cell viability

Enriching a biomaterial surface with specific chemical groups has previously been considered for producing surfaces that influence cell response. Silane layer deposition has previously been shown to control mesenchymal stem cell adhesion and differentiation. However, it has not been used to investigate neuronal or Schwann cell responses in vitro to date. We report on the deposition of aminosilane groups for peripheral neurons and Schwann cells studying two chain lengths: (a) 3-aminopropyl triethoxysilane (short chain-SC) and (b) 11-aminoundecyltriethoxysilane (long chain-LC) by coating glass substrates. Surfaces were characterised by water contact angle, AFM and XPS. LC-NH₂ was produced reproducibly as a homogenous surface with controlled nanotopography. Primary neuron and NG108-15 neuronal cell differentiation and primary Schwann cell responses were investigated in vitro by S100β, p75, and GFAP antigen expression. Both amine silane surface supported neuronal and Schwann cell growth; however, neuronal differentiation was greater on LC aminosilanes versus SC. Thus, we report that silane surfaces with an optimal chain length may have potential in peripheral nerve repair for the modification and improvement of nerve guidance devices.

Modulation of neuronal cell affinity of composite scaffolds based on polyhydroxyalkanoates and bioactive glasses

The biocompatibility and neuron regenerating properties of various bioactive glass (BG)/polyhydroxyalkanoate (PHA) blend composites were assessed in order to study their suitability for peripheral nerve tissue applications, specifically as lumen structures for nerve guidance conduits. BG/PHA blend composites were fabricated using Bioactive glass® 45 S5 (BG1) and BG 1393 (BG2) with the 25:75 poly(3-hydroxyoctanoate/poly3-hydroxybutyrate), 25:75 P(3HO)/P(3HB) blend (PHA blend). Various concentrations of each BG (0.5 wt%, 1.0 wt% and 2.5 wt%) were used to determine the effect of BG on neuronal growth and differentiation, in single culture using NG108-15 neuronal cells and in a co-culture along with RN22 Schwann cells. NG108-15 cells exhibited good growth and differentiation on all the PHA blend composites showing that both BGs have good biocompatibility at 0.5 wt%, 1.0 wt% and 2.5 wt% within the PHA blend. The Young's modulus values displayed by all the PHA blend/BG composites ranged from 385.6 MPa to 1792.6 MPa, which are able to provide the required support and protective effect for the regeneration of peripheral nerves. More specifically, the tensile strength obtained in the PHA blend/BG1 (1.0 wt%) (10.0 ± 0.6 MPa) was found to be similar to that of the rabbit peroneal nerve. This composite also exhibited the best biological performance in supporting growth and neuronal differentiation among all the substrates. The neurite extension on this composite was found to be remarkable with the neurites forming a complex connection network.

The dynamics of neutrophils in zebrafish (Danio rerio) during infection with the parasite Ichthyophthirius multifiliis

Ichthyophthirius multifiliis is a ciliated protozoan parasite infecting the skin and gills of freshwater fish. Neutrophils are attracted to the infection sites, as a part of the innate immune response. In this study a transgenic line of zebrafish (Tg(MPO:GFP)(i114)) with GFP-tagged neutrophils was infected with I. multifiliis and the neutrophil influx in the caudal fin was quantified. Twenty-four hours post infection (pi) the neutrophil count had gone up with an average of 3.4 fold. Forty-eight h pi the neutrophil count had dropped 12% and 72 h pi it had dropped to 21% compared to 24 h pi. At 72 h pi the neutrophil count was 2.7 times higher than prior to infection. A few dead parasites were observed, which were disintegrated and covered internally and externally with neutrophils. Live parasites, both surrounded by neutrophils and with no neutrophils in the near vicinity, were found during the infection. Neutrophils interacted directly with the parasites with pseudopod formation projecting towards the pathogen. These results indicate a strong innate immune response immediately following infection and/or a subsequent immune evasion by the parasite.

Comparison of two automatic cell-counting solutions for fluorescent microscopic images

Cell counting in microscopic images is one of the fundamental analysis tools in life sciences, but is usually tedious, time consuming and prone to human error. Several programs for automatic cell counting have been developed so far, but most of them demand additional training or data input from the user. Most of them do not allow the users to online monitor the counting results, either. Therefore, we designed two straightforward, simple-to-use cell-counting programs that also allow users to correct the detection results. In this paper, we present the Cellcounter and Learn123 programs for automatic and semiautomatic counting of objects in fluorescent microscopic images (cells or cell nuclei) with a user-friendly interface. Although Cellcounter is based on predefined and fine-tuned set of filters optimized on sets of chosen experiments, Learn123 uses an evolutionary algorithm to determine the adapt filter parameters based on a learning set of images. Cellcounter also includes an extension for analysis of overlaying images. The efficiency of both programs was assessed on images of cells stained with different fluorescent dyes by comparing automatically obtained results with results that were manually annotated by an expert. With both programs, the correlation between automatic and manual counting was very high (R(2) < 0.9), although Cellcounter had some difficulties processing images with no cells or weakly stained cells, where sometimes the background noise was recognized as an object of interest. Nevertheless, the differences between manual and automatic counting were small compared to variations between experimental repeats. Both programs significantly reduced the time required to process the acquired images from hours to minutes. The programs enable consistent, robust, fast and accurate detection of fluorescent objects and can therefore be applied to a range of different applications in different fields of life sciences where fluorescent labelling is used for quantification of various phenomena. Moreover, Cellcounter overlay extension also enables fast analysis of related images that would otherwise require image merging for accurate analysis, whereas Learn123's evolutionary algorithm can adapt counting parameters to specific sets of images of different experimental settings.

Bright field microscopic cells counting method for BEVS using nonlinear convergence index sliding band filter

Background

The Baculovirus Expression Vector System (BEVS) is a very popular expression vector system in gene engineering. An effective host cell line cultivation protocol can facilitate the baculovirus preparation and following experiments. However, the counting of the number of host cells in the protocol is usually performed by manual observation with microscopy, which is time consuming and labor intensive work, and prone to errors for one person or between different individuals. This study aims at giving a bright field insect cells counting protocol to help improve the efficient of BEVS.

Method

To develop a reliable and accurate counting method for the host cells in the bright field, such as Sf9 insect cells, a novel method based on a nonlinear Transformed Sliding Band Filter (TSBF) was proposed. And 3 collaborators counted cells at the same time to produce the ground truth for evaluation. The performance of TSBF method was evaluated with the image datasets of Sf9 insect cells according to the different periods of cell cultivation on the cell density, error rate and growth curve.

Results

The average error rate of our TSBF method is 2.21% on average, ranging from 0.89% to 3.97%, which exhibited an excellent performance with its high accuracy in lower error rate compared with traditional methods and manual counting. And the growth curve was much the manual method well.

Conclusion

Results suggest the proposed TSBF method can detect insect cells with low error rate, and it is suitable for the counting task in BEVS to take the place of manual counting by humans. Growth curve results can reflect the cells’ growth manner, which was generated by our proposed TSBF method in this paper can reflected the similar manner with it’s from the manual method. All of these proven that the proposed insect cell counting method can clearly improve the efficiency of BEVS.

Comparison of flow cytometry, fluorescence microscopy and spectrofluorometry for analysis of gene electrotransfer efficiency

In this study, we compared three different methods used for quantification of gene electrotransfer efficiency: fluorescence microscopy, flow cytometry and spectrofluorometry. We used CHO and B16 cells in a suspension and plasmid coding for GFP. The aim of this study was to compare and analyse the results obtained by fluorescence microscopy, flow cytometry and spectrofluorometry and in addition to analyse the applicability of spectrofluorometry for quantifying gene electrotransfer on cells in a suspension. Our results show that all the three methods detected similar critical electric field strength, around 0.55 kV/cm for both cell lines. Moreover, results obtained on CHO cells showed that the total fluorescence intensity and percentage of transfection exhibit similar increase in response to increase electric field strength for all the three methods. For B16 cells, there was a good correlation at low electric field strengths, but at high field strengths, flow cytometer results deviated from results obtained by fluorescence microscope and spectrofluorometer. Our study showed that all the three methods detected similar critical electric field strengths and high correlations of results were obtained except for B16 cells at high electric field strengths. The results also demonstrated that flow cytometry measures higher values of percentage transfection compared to microscopy. Furthermore, we have demonstrated that spectrofluorometry can be used as a simple and consistent method to determine gene electrotransfer efficiency on cells in a suspension.

Predicting electroporation of cells in an inhomogeneous electric field based on mathematical modeling and experimental CHO-cell permeabilization to propidium iodide determination

High voltage electric pulses cause electroporation of the cell membrane. Consequently, flow of the molecules across the membrane increases. In our study we investigated possibility to predict the percentage of the electroporated cells in an inhomogeneous electric field on the basis of the experimental results obtained when cells were exposed to a homogeneous electric field. We compared and evaluated different mathematical models previously suggested by other authors for interpolation of the results (symmetric sigmoid, asymmetric sigmoid, hyperbolic tangent and Gompertz curve). We investigated the density of the cells and observed that it has the most significant effect on the electroporation of the cells while all four of the mathematical models yielded similar results. We were able to predict electroporation of cells exposed to an inhomogeneous electric field based on mathematical modeling and using mathematical formulations of electroporation probability obtained experimentally using exposure to the homogeneous field of the same density of cells. Models describing cell electroporation probability can be useful for development and presentation of treatment planning for electrochemotherapy and non-thermal irreversible electroporation.

Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images

The quantitative determination of key adherent cell culture characteristics such as confluency, morphology, and cell density is necessary for the evaluation of experimental outcomes and to provide a suitable basis for the establishment of robust cell culture protocols. Automated processing of images acquired using phase contrast microscopy (PCM), an imaging modality widely used for the visual inspection of adherent cell cultures, could enable the non-invasive determination of these characteristics. We present an image-processing approach that accurately detects cellular objects in PCM images through a combination of local contrast thresholding and post hoc correction of halo artifacts. The method was thoroughly validated using a variety of cell lines, microscope models and imaging conditions, demonstrating consistently high segmentation performance in all cases and very short processing times (<1 s per 1,208 × 960 pixels image). Based on the high segmentation performance, it was possible to precisely determine culture confluency, cell density, and the morphology of cellular objects, demonstrating the wide applicability of our algorithm for typical microscopy image processing pipelines. Furthermore, PCM image segmentation was used to facilitate the interpretation and analysis of fluorescence microscopy data, enabling the determination of temporal and spatial expression patterns of a fluorescent reporter. We created a software toolbox (PHANTAST) that bundles all the algorithms and provides an easy to use graphical user interface. Source-code for MATLAB and ImageJ is freely available under a permissive open-source license. Biotechnol. Bioeng. 2014;111: 504–517. © 2013 Wiley Periodicals, Inc.

A robust cell counting approach based on a normalized 2D cross-correlation scheme for in-line holographic images

To achieve the important aims of identifying and marking disease progression, cell counting is crucial for various biological and medical procedures, especially in a Point-Of-Care (POC) setting. In contrast to the conventional manual method of counting cells, a software-based approach provides improved reliability, faster speeds, and greater ease of use. We present a novel software-based approach to count in-line holographic cell images using the calculation of a normalized 2D cross-correlation. This enables fast, computationally-efficient pattern matching between a set of cell library images and the test image. Our evaluation results show that the proposed system is capable of quickly counting cells whilst reliably and accurately following human counting capability. Our novel approach is 5760 times faster than manual counting and provides at least 68% improved accuracy compared to other image processing algorithms.

A cell counting method for BEVS based on nonlinear Transformed Sliding Band Filter

Insect cell is the host of baculovirus in Baculovirus Expression Vector System (BEVS). However, the insect cell counting is an obstacle that constrains the efficiency in BEVS. In this paper, an insect cell counting method based on Transformed Sliding Band Filter (TSBF) was proposed according to insect cell cultivation manner. The proposed method was then applied to insect cell image datasets, and results exhibited that the average relative error rate was 2.21% compared with manual counting. Growth curve evaluation showed that this method was suitable to the protocol of cell cultivation. These exciting results proved that the proposed method was an ideal automatic counting tool for inset cells in BEVS.

Abnormal interneuron development in disrupted-in-schizophrenia-1 L100P mutant mice

Background

Interneuron deficits are one of the most consistent findings in post-mortem studies of schizophrenia patients and are likely important in the cognitive deficits associated with schizophrenia. Disrupted-in-Schizophrenia 1 (DISC1), a strong susceptibility gene for schizophrenia and other mental illnesses, is involved in neurodevelopment, including that of interneurons. However, the mechanism by which DISC1 regulates interneuron development remains unknown. In this study, we analyzed interneuron histology in the Disc1-L100P single point mutation mouse, that was previously shown to have behavioral abnormalities and cortical developmental defects related to schizophrenia.

Results

We sought to determine whether a Disc1-L100P point mutation in the mouse would alter interneuron density and location. First, we examined interneuron position in the developing mouse cortex during embryonic days 14–16 as an indicator of interneuron tangential migration, and found striking migration deficits in Disc1-L100P mutants. Further analysis of adult brains revealed that the Disc1-L100P mutants have selective alterations of calbindin- and parvalbumin-expressing interneurons in the cortex and hippocampus, decreased GAD67/PV co-localization and mis-positioned interneurons across the neocortex when compared to wild-type littermates.

Conclusion

Our results are consistent with the anomalies seen in post-mortem schizophrenia studies and other Disc1 mutant mouse models. Future research is required to determine the specific mechanisms underlying these cellular deficits. Overall, these findings provide further evidence that DISC1 participates in interneuron development and add to our understanding of how DISC1 variants can affect susceptibility to psychiatric illness.

Lucifer Yellow uptake by CHO cells exposed to magnetic and electric pulses

BACKGROUND

The cell membrane acts as a barrier that hinders free entrance of most hydrophilic molecules into the cell. Due to numerous applications in medicine, biology and biotechnology, the introduction of impermeant molecules into biological cells has drawn considerable attention in the past years. One of the most famous methods in this field is electroporation, in which electric pulses with high intensity and short duration are applied to the cells. The aim of our study was to investigate the effect of time-varying magnetic field with different parameters on transmembrane molecular transport.

MATERIALS AND METHODS

'Moreover, a comparison was made between the uptake results due to magnetic pulse exposure and electroporation mediated uptake.' at the end of Background part. The Chinese hamster ovary (CHO) cells were exposed to magnetic pulses of 2.2 T peak strength and 250 μs duration delivered by Magstim stimulator and double 70 mm coil. Three different frequencies of 0.25, 1 and 10 Hz pulses with 112, 56 and 28 number of pulses were applied (altogether nine experimental groups) and Lucifer Yellow uptake was measured in each group. Moreover, maximum uptake of Lucifer Yellow obtained by magnetic pulses was compared to the measured uptake due to electroporation with typical parameters of 8 pulses of 100 μs, repetition frequency of 1 Hz and electric field intensities of 200 to 600 V/cm.

RESULTS AND CONCLUSIONS

Our results show that time-varying magnetic field exposure increases transmembrane molecular transport and this uptake is greater for lower frequencies and larger number of pulses. Besides, the comparison shows that electroporation is more effective than pulsed magnetic field, but the observed uptake enhancement due to magnetic exposure is still considerable.