Semi-automated Counting Research Articles

Sources of Variability in Determinations of Brewing Yeast Total Cell Counts and Viability Obtained by Microscopy

Brewers utilizing yeast cell counts and determinations of yeast viability obtained by microscopy require precise results for calculating the yeast pitch to produce fermentations with the highest quality and consistency. The steps in obtaining results with the desired precision include identifying, quantifying and controlling the sources of variation. In this study, we used simulated cell counting, manual cell counting, and semi-automated cell counting to explore sources of variation contributing to the variability of yeast cell counts and yeast viability determinations. The results showed that the variability associated with counting different fields of view contributed most to the variability in yeast cell counts and determinations of yeast viability. Understanding the sources and amounts of variation in cell counts will help brewers direct their efforts toward obtaining the highest quality determinations of yeast cell counts and viability.

Development of a Semi-Automated Approach for the Quantification of Neuronal Cells in the Spiral Ganglion of the Whole Implanted Gerbil Cochlea, Acquired by Light-Sheet Microscopy.

Assessing cochlear implantation's impact on cell loss and preventing post-implant cochlear damage are key areas of focus for hearing preservation research. The preservation of auditory neuronal and sensory neural hearing cells has a positive impact on auditory perception after implantation. This study aimed to provide details on a semi-automated spiral ganglion neuronal cell counting method, developed using whole implanted gerbil cochlea acquisitions with light-sheet microscopy. Mongolian gerbils underwent right cochlear implantation with an electrode array whose silicone was loaded with dexamethasone or not and were euthanized 10 weeks after implantation. The cochleae were prepared according to a 29-day protocol, with the electrode array in place. Light-sheet microscopy was used for acquisition, and Imaris software was employed for three-dimensional analysis of the cochleas and semi-automatic quantification of spiral ganglion cells. The imaJ software was used for the manual quantification of these cells. Six cochleae were acquired by light-sheet microscopy, allowing good identification of cells. There was no significant difference between the mean number of spiral ganglion cells obtained by manual and semi-automatic counting (p = 0.25). Light-sheet microscopy provided complete visualization of the spiral ganglion and cell identification. The semi-automated counting method developed using Imaris software tools proved reliable and efficient and could be applied to a larger sample to assess post-cochlear implant cell damage and the efficacy of protective drugs delivered to the inner ear.

Comparative Analysis of Laboratory-Based and Spectroscopic Methods Used to Estimate the Algal Density of Chlorella vulgaris.

Chlorella vulgaris is of great importance in numerous exploratory or industrial applications (e.g., medicals, food, and feed additives). Rapid quantification of algal biomass is crucial in photobioreactors for the optimization of nutrient management and the estimation of production. The main goal of this study is to provide a simple, rapid, and not-resource-intensive estimation method for determining the algal density of C. vulgaris according to the measured parameters using UV-Vis spectrophotometry. Comparative assessment measurements were conducted with seven different methods (e.g., filtration, evaporation, chlorophyll a extraction, and detection of optical density and fluorescence) to determine algal biomass. By analyzing the entire spectra of diluted algae samples, optimal wavelengths were determined through a stepwise series of linear regression analyses by a novel correlation scanning method, facilitating accurate parameter estimation. Nonlinear formulas for spectrometry-based estimation processes were derived for each parameter. As a result, a general formula for biomass concentration estimation was developed, with recommendations for suitable measuring devices based on algae concentration levels. New values for magnesium content and the average single-cell weight of C. vulgaris were established, in addition to the development of a rapid, semiautomated cell counting method, improving efficiency and accuracy in algae quantification for cultivation and biotechnology applications.

#439 Nephron number determination in whole slide mice kidney specimens using a deep learning assisted disector/fractionator approach

Abstract Background and Aims Nephron number highly varies between different species and within species, ranging in humans from 200 000 to 2 000 000 nephrons per kidney. Low nephron numbers can promote early onset of end-stage kidney disease. Nephron assessment is highly needed for better diagnosis and more targeted treatment. However, its assessment in vivo is not established in clinical practice yet. Pioneer studies suggest nephron number estimation in vivo through a combination of glomerular densities in kidney biopsies together with medical imaging. In contrast, post-mortem nephron assessment either using optical clearing or by exhaustive kidney sectioning is well studied but remains laborious. Here, we propose a new semi-automated nephron counting approach using serial PAS-stained whole slide kidney sections, deep learning segmentation and slide registration. Method Mice were sacrificed, kidneys harvested, measured, halved in the coronary plane and then opposingly embedded in paraffin. Subsequently, the entire kidney was sectioned with 10 µm thickness per slide. Tissue was stained with PAS and slides were digitalized using Aperio GT 450 DX scanner (Leica, Wetzlar, Germany) (Fig. a). Deep learning segmentation of glomeruli was performed in the first and every 10th (reference) section and subsequent (look-up) section using Tensorflow. Obtained segmentation results were manually quality controlled and adjusted, if necessary, in QuPath (Fig. b). Final segmentations of the look-up slides were registered to the reference slides in ImageJ using manual landmarks with the ImageJ BigWarp plugin (Fig. c). Glomeruli being present either in the look-up slide, or in the reference slide were counted as disector particles (Q-). Kidney areas on every examined slide were measured. Total number of glomeruli and total kidney area were determined as previously described (Fig. d). Results A kidney from a 12-week-old mouse suffering chronic kidney disease (mouse line Alb-creERT2 (ki/ki); Glut9 (fl/fl)) was used. Kidney weight was 162 mg, length 11 mm, width 6 mm, depth 4 mm and kidney volume 260 mm³. In total the kidney was sectioned in 95 slices. 20 reference sections and its respective look-up sections were stained and digitalized. In total 5981 glomeruli were segmented in 40 kidney slices using the deep learning algorithm. Glomerular segmentation quality was verified by two independent observers (mean dice score 0.79). Inaccuracies, if any, where manually corrected. For image registration in average 18.1 landmarks per slide were created within the ImageJ BigWarp plugin. Registration took in average 5 minutes per slide. Glomeruli without match (disector particles, Q-) were automatically counted. Number of disector particles (Q-) ranged from 32 to 244 per slide. Total nephron number was 11.085 and kidney area 210 mm³. The differences to the manual measured volume (260 mm³) might be explained by discard of small kidney fractions for the used sectioning technique. Conclusion We report, to our knowledge, the first deep learning assisted disector/fractionator approach to determine nephron number in whole slide kidney specimens. This method requires no physical disector setup, is scalable, cheap, time efficient, and unbiased. The method was so far validated in a mouse model of chronic kidney disease. The method will further be validated on different animal models. Additionally, occurrence of atubular glomeruli will be considered in nephron number determination. Furthermore, the integration of GFR measurements might allow the calculation of mean single nephron GFR and might together with automated glomerular area measurements unravel pathophysiologic processes in kidney ageing and disease.

Determining differences in the timing of fish feed intake using a novel dual ballotini X-radiography method

Fish feeding behaviour can be complicated and time consuming to observe, analyse and quantify. The conventional single ballotini X-radiography method was modified to determine the timing of feeding within a meal in farmed fish reared at commercial densities. Feed pellets containing two bead sizes were fed at different times during a single meal, either for the first half or second half of the meal. The two different ballotini sizes were differentiated on X-radiographs by human eye and semi-automated bead counting software was able to count the different bead sizes accurately. This dual ballotini method was used to assess whether fish ate earlier, later or during both halves of the meal and showed that individual fish feeding patterns were similar across two repeated meals. The method was applied to Chinook salmon (Oncorhynchus tshawytscha), a premium farmed salmonid, to determine the relationship between feed conversion ratio (FCR) and the timing of feeding. Results showed that fish that ate smaller amounts of feed ate most of their meal at the end of the meal. There was no significant difference in when feed efficient or feed inefficient fish ate within the meal but, at the first dual ballotini assessment, there was a relationship between FCR and the timing of feeding where more efficient fish ate later in the meal. However, this relationship was absent at the second time point. Despite this, the dual ballotini method is a promising and versatile alternative method for the characterisation of fish feeding behaviours and can be applied under a range of conditions including higher rearing densities.

A Chronological Study of the Miocene Shanwang Diatomaceous Shale in Shandong Province, Eastern China

The varve chronological approach has been applied to older ages (pre-Quaternary) in the Shanwang Basin for the first time. This study focuses on the analysis of diatom shale from the Shanwang Basin, which was formed in Maar Lake (a volcanic crater basin, often filled by a lake). The lacustrine sediments of the basin encapsulate comprehensive geological information. By identifying species and providing systematic paleontological descriptions of diatoms in the profile, two genera and seven species were recognized. A microscopic examination of the thin sections revealed five types of laminae and couplets. On this basis, the study adopted the artificial semi-automatic counting method of the laminae. The calculation results show that the age of the diatom shale section in the Shanwang Basin is 18.524–17.985 Myr B.P, the deposition time is 0.54 Myr, and the deposition rate is 4.06 cm/Kyr. Finally, through the comparative discussion of various dating methods, it can be concluded that the varve chronology is a more accurate and reliable dating method than other dating methods. The research findings contribute to our understanding of the geological history of the region.

Prognostic effect of programmed cell death ligand 1/programmed cell death 1 expression in cancer stem cells of human oral squamous cell carcinoma.

The relationship between cancer stem cells (CSCs) in oral squamous cell carcinoma (OSCC) and programmed cell death ligand 1 (PD-L1)/programmed cell death 1 (PD-1) remains unclear. Therefore, the present study aimed to clarify the association between the CD44v3high/CD24low immunophenotype of CSCs in OSCC and PD-L1/PD-1 co-expression, and to assess the prognostic effect of CSCs in terms of immune checkpoint molecules. Formalin-fixed, paraffin-embedded tissue samples and clinicopathological data from 168 patients with OSCC were retrospectively retrieved. Immunohistochemical staining and reverse transcription quantitative polymerase chain reaction were applied to a tissue microarray of the invasive front of each case. Semi-automated cell counting was used to assess CD44v3, CD24, PD-L1 and PD-1 expression by immunohistochemistry (IHC) using a digital image analysis program. Associations between immunological markers and clinicopathological variables were estimated. Patients with the CSC immunophenotype CD44v3high/CD24low, and patients with a high PD-L1/PD-1-positive cell density in the tumor parenchyma and stroma had significantly lower survival rates. Furthermore, patients with the CSC immunophenotype (CD44v3high/CD24low) and high PD-L1/PD-1 co-expression had even lower survival rates (P<0.01, log-rank test). Notably, there was a positive correlation between CD44v3 and PD-L1 expression (τ=0.1096, P=0.0366, Kendall rank correlation coefficient) and a negative correlation between CD24 and PD-1 expression (τ=-0.1387, P=0.0089, Kendall rank correlation coefficient). Additionally, the high CD44v3 expression group, as determined by IHC, exhibited significantly decreased expression of U2 small nuclear RNA auxiliary factor 1 (U2AF1) at the mRNA level compared with that in the low CD44v3 expression group (P<0.001, Mann-Whitney U test), and U2AF1 and PD-L1 mRNA expression exhibited a significant negative correlation (τ=-0.3948, P<0.001, Kendall rank correlation coefficient). In conclusion, CSCs in OSCC may evade host immune mechanisms and maintain CSC stemness via PD-L1/PD-1 co-expression, resulting in unfavorable clinical outcomes.

Quanty-cFOS, a Novel ImageJ/Fiji Algorithm for Automated Counting of Immunoreactive Cells in Tissue Sections.

Analysis of neural encoding and plasticity processes frequently relies on studying spatial patterns of activity-induced immediate early genes' expression, such as c-fos. Quantitatively analyzing the numbers of cells expressing the Fos protein or c-fos mRNA is a major challenge owing to large human bias, subjectivity and variability in baseline and activity-induced expression. Here, we describe a novel open-source ImageJ/Fiji tool, called 'Quanty-cFOS', with an easy-to-use, streamlined pipeline for the automated or semi-automated counting of cells positive for the Fos protein and/or c-fos mRNA on images derived from tissue sections. The algorithms compute the intensity cutoff for positive cells on a user-specified number of images and apply this on all the images to process. This allows for the overcoming of variations in the data and the deriving of cell counts registered to specific brain areas in a highly time-efficient and reliable manner. We validated the tool using data from brain sections in response to somatosensory stimuli in a user-interactive manner. Here, we demonstrate the application of the tool in a step-by-step manner, with video tutorials, making it easy for novice users to implement. Quanty-cFOS facilitates a rapid, accurate and unbiased spatial mapping of neural activity and can also be easily extended to count other types of labelled cells.

External load in male professional volleyball: A systematic review

Introduction. The objectives of this systematic review were to identify the volleyball external loads values in the literature and to verify the applicability of different means of quantification and monitoring of these variables during training sessions and matches. Material and methods: This systematic review was produced following the PRISMA statement recommendations, and the search for publications was carried out in the databases PubMed/NCBI, SportDiscus via EBSCOhost, SciELO. 12 studies meet the criteria and were included in this review. Results: The most used tool for quantification, monitoring and evaluation of external loads are video recording and manual or semi-automatic counting of jumps and distance covered and, more recently, the use of inertial measurements unit. The middle blocker has the highest high jump load, outside hitters jump closer to the maximum more often and setters have a high demand of medium height jumps. Conclusions: Match and training jump loads seem to be similar, and sessions that involve block or attack have a higher jump load. In professional male volleyball, training is planned with variation in training loads according to the period of the sea-son and according to the days of the week before and after games.

Frame Rhythm: A new cost-effective approach for semi-automatic microalgal imaging and enumeration

Quantifying cell abundance is of paramount importance for monitoring the quality and production of microalgal growth, as well as for early detection of harmful algal blooms (HAB) events, which cause economic losses and societal impacts around the globe. Although manual quantification using counting chambers and microscopy is a well-established method to count microalgae, it is very time-consuming and requires an advanced level of expertise. In last decades, a variety of commercial instruments has emerged as an alternative to automate this process. However, their high cost and the need for specialized technical support hamper their dissemination, particularly in developing countries. This study presents a simple, fast, reliable and cost-effective method for semi-automatic microalgae quantification. The so-called Frame Rhythm (FR) method relies on a handcrafted simple counting chamber imaged with a digital camera coupled to a regular microscope. An in-house software subsequently detects and quantifies microalgal cells in an image sequence, preventing repetitive counts and static noise. The proposed approach was validated by comparison with well-established methods, while tracking different growth phases of the chlorophycean Tetraselmis gracilis, a widely cultured microalga. Results indicated a strong positive correlation (r = 0.99, R2 = 98.31%, p ≤ 0.01) and high agreement between methods, as well as low intra (1–11%) and inter-operator (2–12%) variance for the proposed technique. The FR method provided a reduction of at least 14× in sample processing time in relation to traditional microscopy, at a much lower implementation and maintenance cost compared to commercially available automatic and semi-automatic counting equipment. The new method represents an affordable alternative to acquire microalgal abundance data with a similar degree of accuracy compared to traditional counting chambers and sophisticated benchtop instrumentation.

Automatic counting of retinal ganglion cells in the entire mouse retina based on improved YOLOv5.

Glaucoma is characterized by the progressive loss of retinal ganglion cells (RGCs), although the pathogenic mechanism remains largely unknown. To study the mechanism and assess RGC degradation, mouse models are often used to simulate human glaucoma and specific markers are used to label and quantify RGCs. However, manually counting RGCs is time-consuming and prone to distortion due to subjective bias. Furthermore, semi-automated counting methods can produce significant differences due to different parameters, thereby failing objective evaluation. Here, to improve counting accuracy and efficiency, we developed an automated algorithm based on the improved YOLOv5 model, which uses five channels instead of one, with a squeeze-and-excitation block added. The complete number of RGCs in an intact mouse retina was obtained by dividing the retina into small overlapping areas and counting, and then merging the divided areas using a non-maximum suppression algorithm. The automated quantification results showed very strong correlation (mean Pearson correlation coefficient of 0.993) with manual counting. Importantly, the model achieved an average precision of 0.981. Furthermore, the graphics processing unit (GPU) calculation time for each retina was less than 1 min. The developed software has been uploaded online as a free and convenient tool for studies using mouse models of glaucoma, which should help elucidate disease pathogenesis and potential therapeutics.

A robust, semi-automated approach for counting cementum increments imaged with synchrotron X-ray computed tomography.

Cementum, the tissue attaching mammal tooth roots to the periodontal ligament, grows appositionally throughout life, displaying a series of circum-annual incremental features. These have been studied for decades as a direct record of chronological lifespan. The majority of previous studies on cementum have used traditional thin-section histological methods to image and analyse increments. However, several caveats have been raised in terms of studying cementum increments in thin-sections. Firstly, the limited number of thin-sections and the two-dimensional perspective they impart provide an incomplete interpretation of cementum structure, and studies often struggle or fail to overcome complications in increment patterns that complicate or inhibit increment counting. Increments have been repeatedly shown to both split and coalesce, creating accessory increments that can bias increment counts. Secondly, identification and counting of cementum increments using human vision is subjective, and it has led to inaccurate readings in several experiments studying individuals of known age. Here, we have attempted to optimise a recently introduced imaging modality for cementum imaging; X-ray propagation-based phase-contrast imaging (PPCI). X-ray PPCI was performed for a sample of rhesus macaque (Macaca mulatta) lower first molars (n = 10) from a laboratory population of known age. PPCI allowed the qualitative identification of primary/annual versus intermittent secondary increments formed by splitting/coalescence. A new method for semi-automatic increment counting was then integrated into a purpose-built software package for studying cementum increments, to count increments in regions with minimal complications. Qualitative comparison with data from conventional cementochronology, based on histological examination of tissue thin-sections, confirmed that X-ray PPCI reliably and non-destructively records cementum increments (given the appropriate preparation of specimens prior to X-ray imaging). Validation of the increment counting algorithm suggests that it is robust and provides accurate estimates of increment counts. In summary, we show that our new increment counting method has the potential to overcome caveats of conventional cementochronology approaches, when used to analyse three-dimensional images provided by X-ray PPCI.

EEG Biomarkers of Repository Corticotropin Injection Treatment.

Hypsarrhythmia is one of the major diagnostic and treatment response criteria in infantile spasms (IS). The clinical and electrophysiological effect of repository corticotropin injection treatment on IS was evaluated using electrophysiological biomarkers. Consecutive infants (<24 months) treated with repository corticotropin injection for IS were included in this retrospective descriptive study. Inclusion criteria were (1) clinical IS diagnosis, (2) repository corticotropin injection treatment, and (3) consecutive EEG recordings before and after repository corticotropin injection treatment. Patients with tuberous sclerosis complex were excluded. Response to treatment was defined as freedom from IS for at least 7 consecutive days during the treatment and resolution of hypsarrhythmia. The authors defined "relapse" as the recurrence of seizures after an initial response. Electrophysiological biomarker assessment included evaluation of semiautomatic spike counting algorithm, delta power, and delta coherence calculation during non-REM sleep EEG. One hundred fifty patients (83 males; 55%; median age of IS onset: 5.9 months) with complete data were included, including 101 responders (67%, 71 with sustained response, and 30 relapses). Fifty patients (33%) with complete EEG data also underwent advanced EEG analysis. Baseline delta coherence was higher in sustained responders than in nonresponders or patients who relapsed. Greater decreases in semiautomatic spike counting algorithm, delta power, and delta coherence were found in sustained responders compared with nonresponders or patients who relapsed. Repository corticotropin injection treatment was associated with a 67% response rate in patients with IS. Computational biomarkers beyond hypsarrhythmia may provide additional information during IS treatment, such as early determination of treatment response and outcome assessment.

Application Test of the AI-Automatic Diagnostic System for Ki-67 in Breast Cancer

To study the different methods of artificial intelligence (AI)-assisted Ki-67 scoring of clinical invasive ductal carcinoma (IDC) of the breast and to compare the results. A total of 100 diagnosed IDC cases were collected, including slides of HE staining and immunohistochemical Ki-67 staining and diagnosis results. The slides were scanned and turned into whole slide image (WSI), which were then scored with AI. There were two AI scoring methods. One was fully automatic counting by AI, which used the scoring system of Ki-67 automatic diagnosis to do counting with the whole image of WSI. The second method was semi-automatic AI counting, which required manual selection of areas for counting, and then relied on an intelligent microscope to conduct automatic counting. The diagnostic results of pathologists were taken as the results of pure manual counting. Then the Ki-67 scores obtained by manual counting, semi-automatic AI counting and automatic AI counting were pairwise compared. The Ki-67 scores obtained from the manual counting (pathological diagnosis results), semi-automatic AI and automatic AI counts were pair-wise compared and classified according to three levels of difference: difference ≤10%, difference of >10%-<30% and difference ≥30%. Intra-class correlation coefficient ( ICC) was used to evaluate the correlation. The automatic AI counting of Ki-67 takes 5-8 minutes per case, the semi-automatic AI counting takes 2-3 minutes per case, and the manual counting takes 1-3 minutes per case. When results of the two AI counting methods were compared, the difference in Ki-67 scores was all within 10% (100% of the total), and the ICC index being 0.992. The difference between manual counting and semi-automatic AI was less than 10% in 60 cases (60% of the total), between 10% and 30% in 37 cases (37% of the total), and more than 30% in only 3 cases (3% of the total), ICC index being 0.724. When comparing automatic AI with manual counting, 78 cases (78% of the total) had a difference of ≤10%, 17 cases (17% of the total) had a difference of between 10% and 30%, and 5 cases (5%) had a difference of ≥30%, the ICC index being 0.720. The ICC values showed that there was little difference between the results of the two AI counting methods, indicating good repeatability, but the repeatability between AI counting and manual counting was not particularly ideal. AI automatic counting has the advantage of requiring less manpower, for the pathologist is involved only for the verification of the diagnosis results at the end. However, the semi-automatic method is better suited to the diagnostic habits of pathologists and has a shorter turn-over time compared with that of the fully automatic AI counting method. Furthermore, in spite of its higher repeatability, AI counting, cannot serve as a full substitute for pathologists, but should instead be viewed as a powerful auxiliary tool.

Spatial Distribution of Arctic Bacterioplankton Abundance Is Linked to Distinct Water Masses and Summertime Phytoplankton Bloom Dynamics (Fram Strait, 79°N).

The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0–30 m) down to deep waters (2,500 m) in summer ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from 105 cells mL–1 in ice-covered regions to 106 cells mL–1 in the ice-free regions. Observations suggest that these were overall driven by variations in phytoplankton bloom conditions across the Strait. The bacterial groups Bacteroidetes and Gammaproteobacteria showed several-fold higher cell abundances under late phytoplankton bloom conditions of the ice-free regions. Other taxonomic groups, such as the Rhodobacteraceae, revealed a distinct association of cell abundances with the surface Atlantic waters. With increasing depth (>500 m), the total cell abundances of the bacterioplankton communities decreased by up to two orders of magnitude, while largely unknown taxonomic groups (e.g., SAR324 and SAR202 clades) maintained constant cell abundances throughout the entire water column (ca. 103 cells mL–1). This suggests that these enigmatic groups may occupy a specific ecological niche in the entire water column. Our results provide the first quantitative spatial variations assessment of bacterioplankton in the summer ice-covered and ice-free Arctic water column, and suggest that further shift toward ice-free Arctic summers with longer phytoplankton blooms can lead to major changes in the associated standing stock of the bacterioplankton communities.

Semi-automated counting of complex varves through image autocorrelation

AbstractAnnual resolution sediment layers, known as varves, can provide continuous and high-resolution chronologies of sedimentary sequences. In addition, varve counting is not burdened with the high laboratory costs of geochronological analyses. Despite a more than 100-year history of use, many existing varve counting techniques are time consuming and difficult to reproduce. We present countMYvarves, a varve counting toolbox which uses sliding-window autocorrelation to count the number of repeated patterns in core scans or outcrop photos. The toolbox is used to build an annually-resolved record of sedimentation rates, which are depth-integrated to provide ages. We validate the model with repeated manual counts of a high sedimentation rate lake with biogenic varves (Herd Lake, USA) and a low sedimentation rate glacial lake (Lago Argentino, Argentina). In both cases, countMYvarves is consistent with manual counts and provides additional sedimentation rate data. The toolbox performs multiple simultaneous varve counts, enabling uncertainty to be quantified and propagated into the resulting age-depth model. The toolbox also includes modules to automatically exclude non-varved portions of sediment and interpolate over missing or disrupted sediment. CountMYvarves is open source, runs through a graphical user interface, and is available online for download for use on Windows, macOS or Linux at https://doi.org/10.5281/zenodo.4031811.

Counting breeding gulls with unmanned aerial vehicles: camera quality and flying height affects precision of a semi-automatic counting method

The use of Unmanned Aerial Vehicles (UAVs) to monitor large colonies of seabirds avoids challenges associated with conventional methods, but manual image processing is expensive. Development of semi-automated analytical methods rely on high image spatial resolution, which requires a trade-off between securing low area coverage and high spatial resolution flying at low altitude vs high area coverage but low spatial resolution flying at higher altitudes. Increasing individual bird detection probabilities requires maximizing contrast between target and background, which can be enhanced using thermal sensors. We applied a semi-automatic analytical method to multispectral UAV derived imagery to count a mixed breeding colony of Herring Gulls (Larus argentatus) and Lesser Blackbacked Gulls (L. fuscus). We trained the computer to detect different image classes by their spectral signature in several orthomosaics obtained from UAV flights at different altitudes using different cameras. Highest agreement with the manual counts was achieved by low flying (20 m) using the highest camera resolution (97.7 ± 1.1% for the Herring Gulls, omission error 2.6%, commission error 0.5%; 94.8 ± 1.8% for Lesser Black-backed Gulls, omission error 6.5%, commission error 1.6%). Method precision varied between trials, confirming the importance of low altitude flying with high quality cameras, and a 40% reduction in detection noise from adding a thermal sensor.

Corneal endothelial cell loss after trabeculectomy and phacoemulsification in one or two steps: a prospective study

ObjectiveThe objective of this study was to analyse the results of the surgical treatment of coexisting cataract and glaucoma and its effects on corneal endothelial cell density (CECD).MethodsWe include two longitudinal prospective studies: one randomised that included 40 eyes with open angle glaucoma that received one- (n = 20) or two-step (n = 20) phacotrabeculectomy and another that included 20 eyes that received phacoemulsification. We assess the impact of surgery on different clinical variables and in particular in CECD using Confoscan 4™ confocal microscopy and semiautomatic counting methods.ResultsPhacoemulsification and phacotrabeculectomy, but not trabeculectomy, increase significantly best-corrected visual acuity and anterior chamber depth and trabeculectomy and one- or two-step phacotrabeculectomy decreased similarly the intraocular pressure. We document percentages of endothelial cell loss of 3.1%, 17.9%, 31.6% and 42.6% after trabeculectomy, phacoemulsification and one- or two-step phacotrabeculectomy, respectively. The coefficient of variation did not increase significantly after surgery but the percentage of hexagonality decreased significantly after phacoemulsification and after two-step phacotrabeculectomy.ConclusionsTrabeculectomy, phacoemulsification and phacotrabeculectomy are surgical techniques that cause morphological changes and decrease the densities of the corneal endothelial cells. Trabeculectomy produces lesser endothelial cell loss than phacoemulsification, and phacoemulsification lesser cell loss than phacotrabeculectomy. Two-step phacotrabeculectomy (trabeculectomy followed 3 months later by phacoemulsification) causes more cell loss than one-step phacotrabeculectomy, and this could be due to the cumulative effects of two separate surgical traumas or to a negative conditioning lesion effect of the first surgery. For the treatment of coexisting glaucoma and cataract, one-step phacotrabeculectomy is the treatment of choice.

Intraobserver reproducibility of Ki-67 assessment of breast cancers based on digital slide

Objective: To investigate the intra-observer reproducibility of Ki-67 assessment in breast cancers using three methods based on digital slide. Methods: Thirty cases of invasive breast cancer tissues were immunostained for Ki-67 by automatic stainer, and then scanned into digital pathological slides. Ki-67 positive index was measured individually by three pathologists using size-set visual assessment of hot spot (SSVAHS), size-set semi-automatic counting of hot spot(SSSACHS), and size-set automatic counting of hot spot (SSACHS), respectively, and repeated for 10 times. Intraclass correlation coefficient (ICC) of each assessment method was calculated, and the intraobserver reliability was classified as excellent, good, fair and poor according to ICC. Results: The ICC by 3 pathologists using SSVAHS was 0.832, 0.843 and 0.826, respectively, The ICC using SSSACHS was 0.926,0.938,0.929, and the ICC using SSACHS was 0.964, 0.971 and 0.968.The intraobserver reliability level of all three methods was excellent. Conclusion: The three methods of Ki-67 assessment achieve satisfactory intraobserver reproducibility, and the order of reproducibility from high to low is SSACHS, SSSACHS, and SSVAHS.

Improving the accuracy of dose estimates from automatically scored dicentric chromosomes by accounting for chromosome number

Purpose The traditional workflow for biological dosimetry based on manual scoring of dicentric chromosomes is very time consuming. Especially for large-scale scenarios or for low-dose exposures, high cell numbers have to be analyzed, requiring alternative scoring strategies. Semi-automatic scoring of dicentric chromosomes provides an opportunity to speed up the standard workflow of biological dosimetry. Due to automatic metaphase and chromosome detection, the number of counted chromosomes per metaphase is variable. This can potentially introduce overdispersion and statistical methods for conventional, manual scoring might not be applicable to data obtained by automatic scoring of dicentric chromosomes, potentially resulting in biased dose estimates and underestimated uncertainties. The identification of sources for overdispersion enables the development of methods appropriately accounting for increased dispersion levels. Materials and methods Calibration curves based on in vitro irradiated (137-Cs; 0.44 Gy/min) blood from three healthy donors were analyzed for systematic overdispersion, especially at higher doses (>2 Gy) of low LET radiation. For each donor, 12 doses in the range of 0–6 Gy were scored semi-automatically. The effect of chromosome number as a potential cause for the observed overdispersion was assessed. Statistical methods based on interaction models accounting for the number of detected chromosomes were developed for the estimation of calibration curves, dose and corresponding uncertainties. The dose estimation was performed based on a Bayesian Markov-Chain-Monte-Carlo method, providing high flexibility regarding the implementation of priors, likelihood and the functional form of the association between predictors and dicentric counts. The proposed methods were validated by simulations based on cross-validation. Results Increasing dose dependent overdispersion was observed for all three donors as well as considerable differences in dicentric counts between donors. Variations in the number of detected chromosomes between metaphases were identified as a major source for the observed overdispersion and the differences between donors. Persisting overdispersion beyond the contribution of chromosome number was modeled by a Negative Binomial distribution. Results from cross-validation suggested that the proposed statistical methods for dose estimation reduced bias in dose estimates, variability between dose estimates and improved the coverage of the estimated confidence intervals. However, the 95% confidence intervals were still slightly too permissive, suggesting additional unknown sources of apparent overdispersion. Conclusions A major source for the observed overdispersion could be identified, and statistical methods accounting for overdispersion introduced by variations in the number of detected chromosomes were developed, enabling more robust dose estimation and quantification of uncertainties for semi-automatic counting of dicentric chromosomes.