Bridging imaging users to imaging analysis - A community survey.

The 'Bridging Imaging Users to Imaging Analysis' survey was conducted in 2022 by the Center for Open Bioimage Analysis (COBA), BioImaging North America (BINA) and the Royal Microscopical Society Data Analysis in Imaging Section (RMS DAIM) to understand the needs of the imaging community. Through multichoice and open-ended questions, the survey inquired about demographics, image analysis experiences, future needs and suggestions on the role of tool developers and users. Participants of the survey were from diverse roles and domains of the life and physical sciences. To our knowledge, this is the first attempt to survey cross-community to bridge knowledge gaps between physical and life sciences imaging. Survey results indicate that respondents' overarching needs are documentation, detailed tutorials on the usage of image analysis tools, user-friendly intuitive software, and better solutions for segmentation, ideally in a format tailored to their specific use cases. The tool creators suggested the users familiarise themselves with the fundamentals of image analysis, provide constant feedback and report the issues faced during image analysis while the users would like more documentation and an emphasis on tool friendliness. Regardless of the computational experience, there is a strong preference for 'written tutorials' to acquire knowledge on image analysis. We also observed that the interest in having 'office hours' to get an expert opinion on their image analysis methods has increased over the years. The results also showed less-than-expected usage of online discussion forums in the imaging community for solving image analysis problems. Surprisingly, we also observed a decreased interest among the survey respondents in deep/machine learning despite the increasing adoption of artificial intelligence in biology. In addition, the community suggests the need for a common repository for the available image analysis tools and their applications. The opinions and suggestions of the community, released here in full, will help the image analysis tool creation and education communities to design and deliver the resources accordingly.

Bridging Imaging Users to Imaging Analysis - A community survey.

The "Bridging Imaging Users to Imaging Analysis" survey was conducted in 2022 by the Center for Open Bioimage Analysis (COBA), Bioimaging North America (BINA), and the Royal Microscopical Society Data Analysis in Imaging Section (RMS DAIM) to understand the needs of the imaging community. Through multi-choice and open-ended questions, the survey inquired about demographics, image analysis experiences, future needs, and suggestions on the role of tool developers and users. Participants of the survey were from diverse roles and domains of the life and physical sciences. To our knowledge, this is the first attempt to survey cross-community to bridge knowledge gaps between physical and life sciences imaging. Survey results indicate that respondents' overarching needs are documentation, detailed tutorials on the usage of image analysis tools, user-friendly intuitive software, and better solutions for segmentation, ideally in a format tailored to their specific use cases. The tool creators suggested the users familiarize themselves with the fundamentals of image analysis, provide constant feedback, and report the issues faced during image analysis while the users would like more documentation and an emphasis on tool friendliness. Regardless of the computational experience, there is a strong preference for 'written tutorials' to acquire knowledge on image analysis. We also observed that the interest in having 'office hours' to get an expert opinion on their image analysis methods has increased over the years. In addition, the community suggests the need for a common repository for the available image analysis tools and their applications. The opinions and suggestions of the community, released here in full, will help the image analysis tool creation and education communities to design and deliver the resources accordingly.

Impact of and Response to Cyberattacks in Radiation Oncology.

Cyberattacks on health care facilities are increasing and significantly affecting health care delivery throughout the world. The recent cyberattack on our hospital-based radiation facility exposed vulnerabilities of radiation oncology systems and highlighted the dependence of radiation treatment on integrated and complex radiation planning, delivery and verification systems. After the cyberattack on our health care facility, radiation oncology staff reconstructed patient information, schedules, and radiation plans from existing paper records and physicians developed a system to triage patients requiring immediate transfer of radiation treatment to nearby facilities. Medical physics and hospital information technology collaborated to restore services without access to the system backup or network connectivity. Ultimately, radiation treatments resumed incrementally as systems were restored and rebuilt. The experiences and lessons learned from this response were reviewed. The successes and shortcomings were incorporated into recommendations to provide guidance to other radiation facilities in preparation for a possible cyberattack. Our response and recommendations are intended to serve as a starting point to assist other facilities in cybersecurity preparedness planning. Because there is no one-size-fits-all response, each department should determine its specific vulnerabilities, risks, and available resources to create an individualized plan.

Ultrasound for the Objective Measurement of Breast Lymphedema.

OBJECTIVES: Breast lymphedema has supplanted upper extremity lymphedema as a common and debilitating sequela of breast cancer treatment, but has no objective measurement. We assessed the utility of ultrasound-measured difference in dermal thickness between affected and unaffected breasts as a measure of breast lymphedema. We associated this measure with patient characteristics, treatment parameters, and patient-reported impact on quality of life. METHODS: We enrolled 30 invasive breast carcinoma patients treated with breast-conserving surgery, sentinel lymph node biopsy, and radiotherapy, and 10 control patients evaluated for benign breast conditions without prior breast surgery or radiotherapy. Patient and treatment variables were ascertained from medical records and radiotherapy instruments. Impacts on quality of life were measured with a modified Disability of the Arm, Shoulder, and Hand questionnaire. We characterized breast lymphedema by calculating the difference in ultrasound-measured dermal thickness between affected and unaffected breasts. Associations with patient characteristics, treatment, and quality of life were quantified with log-binomial regression models. RESULTS: Breast lymphedema was defined as a dermal thickness difference of >0.3 mm. Nineteen patients in the invasive group (63%) had breast lymphedema by this definition. We observed positive associations between ultrasound-defined breast lymphedema and surgical factors (size of primary tumor, number of lymph nodes removed), radiotherapy factors (breast volume irradiated, receipt of radiation boost), and patient-reported outcomes (sleep quality and overall confidence). CONCLUSIONS: Difference in dermal thickness is an easy and inexpensive measurement for quantifying breast lymphedema, and correlates with treatment parameters and patient-reported impacts on quality of life.

Neuronal Graphs: A Graph Theory Primer for Microscopic, Functional Networks of Neurons Recorded by Calcium Imaging.

Connected networks are a fundamental structure of neurobiology. Understanding these networks will help us elucidate the neural mechanisms of computation. Mathematically speaking these networks are "graphs"-structures containing objects that are connected. In neuroscience, the objects could be regions of the brain, e.g., fMRI data, or be individual neurons, e.g., calcium imaging with fluorescence microscopy. The formal study of graphs, graph theory, can provide neuroscientists with a large bank of algorithms for exploring networks. Graph theory has already been applied in a variety of ways to fMRI data but, more recently, has begun to be applied at the scales of neurons, e.g., from functional calcium imaging. In this primer we explain the basics of graph theory and relate them to features of microscopic functional networks of neurons from calcium imaging-neuronal graphs. We explore recent examples of graph theory applied to calcium imaging and we highlight some areas where researchers new to the field could go awry.

Author Correction: Adaptive prospective optical gating enables day-long 3D time-lapse imaging of the beating embryonic zebrafish heart.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images.

Quantification and modelling of curvilinear structures in 2D and 3D images is a common challenge in a wide range of biomedical applications. Image enhancement is a crucial pre-processing step for curvilinear structure quantification. Many of the existing state-of-the-art enhancement approaches still suffer from contrast variations and noise. In this paper, we propose to address such problems via the use of a multiscale image processing approach, called Multiscale Top-Hat Tensor (MTHT). MTHT produces a better quality enhancement of curvilinear structures in low contrast and noisy images compared with other approaches in a range of 2D and 3D biomedical images. The proposed approach combines multiscale morphological filtering with a local tensor representation of curvilinear structure. The MTHT approach is validated on 2D and 3D synthetic and real images, and is also compared to the state-of-the-art curvilinear structure enhancement approaches. The obtained results demonstrate that the proposed approach provides high-quality curvilinear structure enhancement, allowing high accuracy segmentation and quantification in a wide range of 2D and 3D image datasets.

Adaptive prospective optical gating enables day-long 3D time-lapse imaging of the beating embryonic zebrafish heart.

Three-dimensional fluorescence time-lapse imaging of the beating heart is extremely challenging, due to the heart's constant motion and a need to avoid pharmacological or phototoxic damage. Although real-time triggered imaging can computationally "freeze" the heart for 3D imaging, no previous algorithm has been able to maintain phase-lock across developmental timescales. We report a new algorithm capable of maintaining day-long phase-lock, permitting routine acquisition of synchronised 3D + time video time-lapse datasets of the beating zebrafish heart. This approach has enabled us for the first time to directly observe detailed developmental and cellular processes in the beating heart, revealing the dynamics of the immune response to injury and witnessing intriguing proliferative events that challenge the established literature on cardiac trabeculation. Our approach opens up exciting new opportunities for direct time-lapse imaging studies over a 24-hour time course, to understand the cellular mechanisms underlying cardiac development, repair and regeneration.

Active Surveillance for Medically Inoperable Stage IA Lung Cancer in the Elderly.

Objectives Treatment for stage IA lung cancer may be too aggressive an approach in elderly patients with competing co-morbidities. We report outcomes for those electing active surveillance (AS) and investigate factors that may predict indolent disease. Materials and methods Retrospective review was performed for 12 consecutive patients, ≥70 years old, with medically inoperable stage IA, T1N0M0 lung cancer and significant co-morbidities, who chose AS with radiation therapy (RT) reserved for clear disease progression. Collected data included Charlson-Deyo Comorbidity Index (CDCI) grades, histology, and tumor size changes. Volume doubling time (VDT) calculations used a modified Schwartz equation. Results Fifteen nodules underwent AS in 12 patients; three patients had more than one nodule. Median age of all patients was 78 (range, 71-85). All patients' CDCI grades were ≥1, 7 were ≥2. Eleven of 12 patients were deemed to be at high-risk for falls. Twelve nodules in 12 patients were biopsied; adenocarcinoma the prevailing common (47%) histology. The median, one, two and three year patient freedom-from-RT values were 21.4 months (95% CI: 11.6-not reached), 81%, 43%, and 29%, respectively. Median VDT of treated vs. untreated nodules was 189 days (range, 62-infinite) vs. 1153 days (range, 504-infinite), respectively. No patient progressed regionally or distantly, and there have been no cancer-related deaths. Due to cardiovascular events, two patients died and one remains on hospice. Median duration of AS for those still continuing computed tomography (CT) surveillance is 35.1 months. Conclusion Selected elderly patients with stage IA lung cancer and significant co-morbidities may undergo AS without detriment in outcome. Prospective AS studies are warranted.

Extracting 3D Parametric Curves from 2D Images of Helical Objects.

Helical objects occur in medicine, biology, cosmetics, nanotechnology, and engineering. Extracting a 3D parametric curve from a 2D image of a helical object has many practical applications, in particular being able to extract metrics such as tortuosity, frequency, and pitch. We present a method that is able to straighten the image object and derive a robust 3D helical curve from peaks in the object boundary. The algorithm has a small number of stable parameters that require little tuning, and the curve is validated against both synthetic and real-world data. The results show that the extracted 3D curve comes within close Hausdorff distance to the ground truth, and has near identical tortuosity for helical objects with a circular profile. Parameter insensitivity and robustness against high levels of image noise are demonstrated thoroughly and quantitatively.

Racial Disparities in Hypofractionated Radiotherapy Breast Cancer Clinical Trials.

There is a paucity of data regarding factors affecting enrollment onto radiation oncology clinical trials. The purpose of this study was to determine patients and tumor characteristics that influenced enrollment of breast cancer patients onto hypofractionated breast radiotherapy trials (HBRTs) at a single institution. In this retrospective cohort study, patients enrolled on HBRTs at the Rutgers Cancer Institute of New Jersey (n = 132) were compared with a cohort of breast cancer patients eligible for, but not enrolled onto HBRTs treated during the same time period (n = 132). Charts were retrospectively reviewed to determine patients' demographics, clinico-pathologic factors, and treatment characteristics. Statistical analysis was performed to analyze variables affecting enrollment onto HBRTs between the two groups. Over a 42-month time period, 132 patients treated on HBRTs received 2,475-4,995 cGy over 3 to 15 fractions. When compared with patients treated off trial, there was no statistically significant effect of age, family history, lymph node positivity, tumor grade, estrogen or Her-2 receptor status, use of chemotherapy or hormones, use of brachytherapy, or the site of initial consultation on HBRT enrollment. Non-White women were less likely to enroll in HBRT's when compared with White women (25.7% versus 40.1%, p = 0.0129), though this was found to be a nonsignificant trend when taking stage into consideration on multivariate analysis (OR for lower T-stage: 0.281, p = 0.003, OR 1.839 for white race, p = 0.076). Consistent with previous studies, non-White women were less likely to enroll in HBRTs than White women. However, disease stage accounted for these racial disparities. Further studies must be performed to determine if race is an independent factor determining radiation oncology clinical trial enrollment.

Blobs and curves: object-based colocalisation for plant cells.

Blobs and curves occur everywhere in plant bioimaging: from signals of fluorescence-labelled proteins, through cytoskeletal structures, nuclei staining and cell extensions such as root hairs. Here we look at the problem of colocalisation of blobs with blobs (protein-protein colocalisation) and blobs with curves (organelle-cytoskeleton colocalisation). This article demonstrates a clear quantitative alternative to pixel-based colocalisation methods and, using object-based methods, can quantify not only the level of colocalisation but also the distance between objects. Included in this report are computational algorithms, biological experiments and guidance for those looking to increase their use of computationally-based and quantified analysis of bioimages.

Comparison of the effects of phosphate-coated and sandblasted acid-etched titanium implants on osseointegration: a microcomputed tomographic examination in the canine model.

PURPOSE: This study tested the effects of phosphate treatment of titanium on bone volume fraction (BV/TV) at 30 to 60 Μm from the implant surface using microcomputed tomography to analyze the mineralized tissue. MATERIALS AND METHODS: Electrolytically phosphated (50/100 volts [T1/T2]) or nonphosphated 3.3- X 8-mm titanium implants (C) with sandblasted acid-etched surfaces were placed in 40 mandibular sites in five foxhounds 6 weeks after the extraction of the premolars. After 4 weeks, the animals were sacrificed, and BV/TV was analyzed using microcomputed tomography. RESULTS: The mean BV/TV (± standard deviation) of the control implants was 31.4% ± 15.3% (range, 10.9% to 55.3%). For the T1 implants, a mean BV/TV of 38.4% ± 10.7% (range, 21.6% to 57.3%) was seen, and for T2 implants, the mean BV/TV was 40.3% ± 15.1% (range, 16.5% to 61.1%). Mean BV/TV values for the groups were not significantly different. For all groups (C, T1, and T2), there were no significant differences in BV/TV at the most coronal slices. For all groups, there was a positive slope showing more bone apposition as the slices moved from coronal to apical. The T2 group showed significantly increased mineralized tissue moving from the coronal to the apical section of the implant, compared to the control and T1 implants. CONCLUSION: Access to better blood supply and bone cells from the marrow spaces in the apical regions may lead to a better trabecular bone response. Increased mineralized tissue apposition may allow for accelerated loading and more predictable implant placement in sites with poor quality bone or patients with compromised bone healing.

Effect of phosphate treatment of Acid-etched implants on mineral apposition rates near implants in a dog model.

PURPOSE: This study evaluated the effects of phosphate coating of acid-etched titanium on the mineral apposition rate (MAR) and new bone-to-implant contact (BIC) in a canine model. MATERIALS AND METHODS: Titanium implants (2.2 3 4 mm) with acid-etched surfaces that were electrolytically phosphated or not were placed in 48 mandibular sites in six foxhounds. Tetracycline and calcein dyes were administered 1 week after implant placement and 1 week before sacrifice. At 12 weeks after implant placement, the animals were sacrificed. MAR and BIC were evaluated using fluorescence microscopy. Light microscopic and histologic evaluations were performed on undecalcified sections. RESULTS: Microscopic evaluation showed the presence of healthy osteoblasts lining bone surfaces near implants. Similar BIC was observed in phosphated and nonphosphated titanium implant sites. MAR was significantly higher around the nonphosphated titanium implant surfaces than around the phosphated titanium samples. No significant differences were found between dogs or implant sites. CONCLUSION: Acid-etched implants showed significantly higher MARs compared to acid-etched, phosphate-coated implants. Int J Maxillofac Implants 2010;25:278-286.

Unresectable carcinoma of the paranasal sinuses: outcomes and toxicities.

PURPOSE: To evaluate long-term outcomes and toxicity in patients with unresectable paranasal sinus carcinoma treated with radiotherapy, with or without chemotherapy. METHODS AND MATERIALS: Between January 1990 and December 2006, 39 patients with unresectable Stage IVB paranasal sinus carcinoma were treated definitively with chemotherapy plus radiotherapy (n = 35, 90%) or with radiotherapy alone (n = 4, 10%). Patients were treated with three-dimensional conformal radiotherapy (n = 18, 46%), intensity-modulated radiotherapy (n = 12, 31%), or conventional radiotherapy (n = 9, 23%) to a median treatment dose of 70 Gy. Most patients received concurrent platinum-based chemotherapy (n = 32, 82%) and/or concomitant boost radiotherapy (n = 29, 74%). RESULTS: With a median follow-up of 90 months, the 5-year local progression-free survival, regional progression-free survival, distant metastasis-free survival, disease-free survival, and overall survival were 21%, 61%, 51%, 14%, and 15%, respectively. Patients primarily experienced local relapse (n = 25, 64%), mostly within the irradiated field (n = 22). Nine patients developed neck relapses; however none of the 4 patients receiving elective neck irradiation had a nodal relapse. In 13 patients acute Grade 3 mucositis developed. Severe late toxicities occurred in 2 patients with radionecrosis and 1 patient with unilateral blindness 7 years after intensity-modulated radiation therapy (77 Gy to the optic nerve). The only significant factor for improved local progression-free survival and overall survival was a biologically equivalent dose of radiation >/=65 Gy. CONCLUSIONS: Treatment outcomes for unresectable paranasal sinus carcinoma are poor, and combined-modality treatment is needed that is both more effective and associated with less morbidity. The addition of elective neck irradiation may improve regional control.

Effects of phosphated titanium and enamel matrix derivatives on osteoblast behavior in vitro.

PURPOSE: The purpose of this study was to evaluate the effects of phosphated titanium and enamel matrix derivatives (EMD) on osteoblast function. MATERIALS AND METHODS: Primary rat osteoblasts were cultured on disks of either phosphated or nonphosphated titanium. In half of the samples 180 microg of EMD was immediately added. The medium was changed every 2 days for 28 days and then analyzed using transforming growth factor-beta1 (TGF-beta1) and interleukin-1beta (IL-1beta) enzyme-linked immunosorbent assays (ELISAs). Scanning electron microscopy and light microscopy were used to evaluate nodule formation and mineralization. RESULTS: Microscopic evaluation revealed no differences in osteoblast attachment between the 4 groups. Osteoblast nodule formation was observed in all groups. In the absence of mineralizing media, nodules on the nonphosphated titanium samples showed no evidence of mineralization. All nodules on the phosphated titanium had evidence of mineralization. ELISA revealed no significant differences in IL-1beta production between any of the groups. The EMD-treated osteoblasts produced significantly more TGF-beta1 than non-EMD-treated cells for up to 8 days, and osteoblasts on phosphated titanium produced significantly more TGF-beta1 at 8 days. DISCUSSION AND CONCLUSION: Osteoblast attachment appeared unaffected by surface treatment. EMD initiated early TGF-beta1 production, but production decreased to control levels within 10 days. Phosphated titanium increased TGF-beta1 production at 8 days and induced nodule mineralization even in the absence of mineralizing medium.