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  1. Article ; Online: Adrenal lesion classification with abdomen caps and the effect of ROI size.

    Solak, Ahmet / Ceylan, Rahime / Bozkurt, Mustafa Alper / Cebeci, Hakan / Koplay, Mustafa

    Physical and engineering sciences in medicine

    2023  Volume 46, Issue 2, Page(s) 865–875

    Abstract: Accurate classification of adrenal lesions on magnetic resonance (MR) images are very important for diagnosis and treatment planning. The detection and classification of lesions in medical imaging heavily rely on several key factors, including the ... ...

    Abstract Accurate classification of adrenal lesions on magnetic resonance (MR) images are very important for diagnosis and treatment planning. The detection and classification of lesions in medical imaging heavily rely on several key factors, including the specialist's level of experience, work intensity, and fatigue of the clinician. These factors are critical determinants of the accuracy and effectiveness of the diagnostic process, which in turn has a direct impact on patient health outcomes. With the spread of artificial intelligence, the use of computer-aided diagnosis (CAD) systems in disease diagnosis has also increased. In this study, adrenal lesion classification was performed using deep learning on MR images. The data set used was obtained from the Department of Radiology, Faculty of Medicine, Selcuk University, and all adrenal lesions were identified and reviewed in consensus by two radiologists experienced with abdominal MR. Studies were carried out on two different data sets created by T1- and T2-weighted MR images. The data set consisted of 112 benign and 10 malignant lesions for each mode. Experiments were performed with regions of interest (ROIs) of different sizes to increase the working performance. Thus, the effect of the selected ROI size on the classification performance was assessed. In addition, instead of the convolutional neural network (CNN) models used in deep learning, a unique classification model structure called Abdomen Caps was proposed. When the data sets used in classification studies are manually separated for training, validation, and testing, different results are obtained with different data sets for each stage. To eliminate this imbalance, tenfold cross-validation was used in this study. The best results obtained were 0.982, 0.999, 0.969, 0.983, 0.998, and 0.964 for accuracy, precision, recall, F1-score, area under the curve (AUC) score, and kappa score, respectively.
    MeSH term(s) Humans ; Deep Learning ; Artificial Intelligence ; Magnetic Resonance Imaging/methods ; Radiology ; Abdomen
    Language English
    Publishing date 2023-04-25
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2662-4737
    ISSN (online) 2662-4737
    DOI 10.1007/s13246-023-01259-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: ZAF, the first open source fully automated feeder for aquatic facilities.

    Lange, Merlin / Solak, AhmetCan / Vijay Kumar, Shruthi / Kobayashi, Hirofumi / Yang, Bin / Royer, Loïc Alain

    eLife

    2021  Volume 10

    Abstract: In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing aquatic facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, a ... ...

    Abstract In the past few decades, aquatic animals have become popular model organisms in biology, spurring a growing need for establishing aquatic facilities. Zebrafish are widely studied and relatively easy to culture using commercial systems. However, a challenging aspect of maintaining aquatic facilities is animal feeding, which is both time- and resource-consuming. We have developed an open-source fully automatic daily feeding system, Zebrafish Automatic Feeder (ZAF). ZAF is reliable, provides a standardized amount of food to every tank, is cost-efficient and easy to build. The advanced version, ZAF+, allows for the precise control of food distribution as a function of fish density per tank, and has a user-friendly interface. Both ZAF and ZAF+ are adaptable to any laboratory environment and facilitate the implementation of aquatic colonies. Here, we provide all blueprints and instructions for building the mechanics, electronics, fluidics, as well as to setup the control software and its user-friendly graphical interface. Importantly, the design is modular and can be scaled to meet different user needs. Furthermore, our results show that ZAF and ZAF+ do not adversely affect zebrafish culture, enabling fully automatic feeding for any aquatic facility.
    MeSH term(s) Animal Feed ; Animals ; Aquaculture/instrumentation ; Aquaculture/methods ; Automation/instrumentation ; Automation/methods ; Data Collection ; Feeding Behavior ; Software ; Zebrafish/physiology
    Language English
    Publishing date 2021-12-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.74234
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Image Deconvolution via Noise-Tolerant Self-Supervised Inversion

    Kobayashi, Hirofumi / Solak, Ahmet Can / Batson, Joshua / Royer, Loic A.

    2020  

    Abstract: We propose a general framework for solving inverse problems in the presence of noise that requires no signal prior, no noise estimate, and no clean training data. We only require that the forward model be available and that the noise be statistically ... ...

    Abstract We propose a general framework for solving inverse problems in the presence of noise that requires no signal prior, no noise estimate, and no clean training data. We only require that the forward model be available and that the noise be statistically independent across measurement dimensions. We build upon the theory of $\mathcal{J}$-invariant functions (Batson & Royer 2019, arXiv:1901.11365) and show how self-supervised denoising \emph{\`a la} Noise2Self is a special case of learning a noise-tolerant pseudo-inverse of the identity. We demonstrate our approach by showing how a convolutional neural network can be taught in a self-supervised manner to deconvolve images and surpass in image quality classical inversion schemes such as Lucy-Richardson deconvolution.
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing ; Physics - Instrumentation and Detectors
    Subject code 006
    Publishing date 2020-06-10
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Is pelvic mapping applicable in iliosacral screw fixation to determine screw entry point and screw trajectory?

    Durusoy, Serhat / Paksoy, Ahmet Emre / Korkmaz, Murat / Solak, Ahmet Şükrü / Dağlar, Bülent

    Eklem hastaliklari ve cerrahisi = Joint diseases & related surgery

    2019  Volume 30, Issue 3, Page(s) 252–258

    Abstract: Objectives: This study aims to investigate if pelvic mapping is applicable in iliosacral screw fixation to determine screw entry point and screw trajectory.: Patients and methods: Clinical files and images of 16 patients (10 males, 6 females; mean ... ...

    Abstract Objectives: This study aims to investigate if pelvic mapping is applicable in iliosacral screw fixation to determine screw entry point and screw trajectory.
    Patients and methods: Clinical files and images of 16 patients (10 males, 6 females; mean age 35 years; range, 20 to 57 years) who underwent iliosacral screw fixation due to sacroiliac joint injury and sacrum fracture were retrospectively reviewed. Pelvic mapping was performed using preoperative tomography images of the patients and appropriate screw entry point and trajectory were determined. Postoperative computed tomography scans of all patients were obtained and these were used to evaluate the accuracy of the screw position.
    Results: No intraoperative complications occurred. The entry points and trajectory of the screws were compatible for all patients pre- and postoperatively.
    Conclusion: Mapping of the pelvis is a method that can be used for preoperative planning of iliosacral screwing.
    MeSH term(s) Adult ; Bone Screws ; Female ; Fracture Fixation, Internal ; Humans ; Male ; Middle Aged ; Preoperative Care ; Radiography ; Retrospective Studies ; Sacroiliac Joint/diagnostic imaging ; Sacroiliac Joint/injuries ; Sacroiliac Joint/surgery ; Sacrum/diagnostic imaging ; Sacrum/injuries ; Sacrum/surgery ; Spinal Fractures/diagnostic imaging ; Spinal Fractures/surgery ; Young Adult
    Language English
    Publishing date 2019-10-24
    Publishing country Turkey
    Document type Journal Article
    ISSN 1309-0313
    ISSN (online) 1309-0313
    DOI 10.5606/ehc.2019.66489
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: DaXi-high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy.

    Yang, Bin / Lange, Merlin / Millett-Sikking, Alfred / Zhao, Xiang / Bragantini, Jordão / VijayKumar, Shruthi / Kamb, Mason / Gómez-Sjöberg, Rafael / Solak, Ahmet Can / Wang, Wanpeng / Kobayashi, Hirofumi / McCarroll, Matthew N / Whitehead, Lachlan W / Fiolka, Reto P / Kornberg, Thomas B / York, Andrew G / Royer, Loic A

    Nature methods

    2022  Volume 19, Issue 4, Page(s) 461–469

    Abstract: The promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet ... ...

    Abstract The promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet microscope design based on oblique plane illumination that achieves: (1) a wider field of view and high-resolution imaging via a custom remote focusing objective; (2) fast volumetric imaging over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller image coverage for large samples via multi-view imaging and (4) higher throughput multi-well imaging via remote coverslip placement. Our instrument achieves a resolution of 450 nm laterally and 2 μm axially over an imaging volume of 3,000 × 800 × 300 μm. We demonstrate the speed, field of view, resolution and versatility of our instrument by imaging various systems, including Drosophila egg chamber development, zebrafish whole-brain activity and zebrafish embryonic development - up to nine embryos at a time.
    MeSH term(s) Animals ; Brain/diagnostic imaging ; Drosophila ; Embryonic Development ; Microscopy, Fluorescence/methods ; Zebrafish
    Language English
    Publishing date 2022-03-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01417-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Systematic triage and treatment of earthquake victims: Our experience in a tertiary hospital after the 2023 Kahramanmaras earthquake.

    Özdemir, Güzelali / Karlıdağ, Taner / Bingöl, Olgun / Sarıkaya, Baran / Çağlar, Ceyhun / Bozkurt, İbrahim / Akkurt, Mehmet Orçun / Mantı, Nurettin / Gencer, Batuhan / Biçici, Vedat / Çepni, Şahin / Köse, Cem Cüneyt / Doğan, Özgür / İnci, Fatih / Ceyhan, Erman / Yavuz, İbrahim Alper / Gülçek, Murat / Alkan, Hilmi / Turan, Sualp /
    Kılıçaslan, Kasım / Doğan, Metin / Özkurt, Bülent / Tecimel, Osman / Solak, Ahmet Şükrü / Uluyardımcı, Enes / Özaslan, Halil İbrahim / Bozer, Merve / Güven, Şahan / Erdem, Enis / Ülgen, Nuri Koray / Aydın, Tahsin / Güllerci, Ali Murat / Keskin, Ömer Halit

    Joint diseases and related surgery

    2023  Volume 34, Issue 2, Page(s) 480–487

    Abstract: Objectives: The aim of this study was to evaluate the benefits of our triage system in acceleration of intervention for the musculoskeletal injuries and clinical follow-ups of trauma patients admitted to our center after the Kahramanmaras earthquake.: ...

    Abstract Objectives: The aim of this study was to evaluate the benefits of our triage system in acceleration of intervention for the musculoskeletal injuries and clinical follow-ups of trauma patients admitted to our center after the Kahramanmaras earthquake.
    Patients and methods: Between February 6
    Results: Of the patients, 16.2% were children. Lower limb injuries constituted 59.07% of musculoskeletal injuries. Upper limb, pelvic, and spinal cord injuries were observed in 21.9%, 12.7%, and 6.25%, respectively. Conservative treatment was applied to 183 (41.68%) patients. The most common surgical intervention was debridement (n=136, 53.1%). External fixation was applied in the first stage to 21 (8.2%) patients with open fractures. The mean removal time from the rubbles was 32.1±29.38 h. A total of 118 limb fasciotomy operations were applied to the patients. Fifty limb amputations were performed in 40 patients at the last follow-up due to vascular insufficiency and infection.
    Conclusion: Based on our study results, we believe that a triage system using a good communication and organization strategy is beneficial to prevent treatment delay and possible adverse events in future disasters.
    MeSH term(s) Child ; Male ; Female ; Humans ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Triage ; Tertiary Care Centers ; Retrospective Studies ; Earthquakes ; Fractures, Open ; Musculoskeletal Diseases
    Language English
    Publishing date 2023-05-18
    Publishing country Turkey
    Document type Journal Article
    ISSN 2687-4792
    ISSN (online) 2687-4792
    DOI 10.52312/jdrs.2023.1102
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Amniotic fluid angiogenin levels are decreased in pregnancies with fetal trisomy 21.

    Demir, Ahmet / Guclu, Serkan / Bige, Ozgur / Solak, Ahmet / Demir, Namik

    Prenatal diagnosis

    2011  Volume 31, Issue 11, Page(s) 1101–1103

    MeSH term(s) Adult ; Amniocentesis ; Amniotic Fluid/metabolism ; Down Syndrome/diagnosis ; Down Syndrome/metabolism ; Enzyme-Linked Immunosorbent Assay/methods ; Female ; Fetal Diseases/diagnosis ; Fetal Diseases/genetics ; Fetal Diseases/metabolism ; Fetus/metabolism ; Fetus/pathology ; Humans ; Infant ; Pregnancy ; Retrospective Studies ; Ribonuclease, Pancreatic/metabolism
    Chemical Substances angiogenin (EC 3.1.27.-) ; Ribonuclease, Pancreatic (EC 3.1.27.5)
    Language English
    Publishing date 2011-11
    Publishing country England
    Document type Letter
    ZDB-ID 82031-3
    ISSN 1097-0223 ; 0197-3851
    ISSN (online) 1097-0223
    ISSN 0197-3851
    DOI 10.1002/pd.2830
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Democratising deep learning for microscopy with ZeroCostDL4Mic.

    von Chamier, Lucas / Laine, Romain F / Jukkala, Johanna / Spahn, Christoph / Krentzel, Daniel / Nehme, Elias / Lerche, Martina / Hernández-Pérez, Sara / Mattila, Pieta K / Karinou, Eleni / Holden, Séamus / Solak, Ahmet Can / Krull, Alexander / Buchholz, Tim-Oliver / Jones, Martin L / Royer, Loïc A / Leterrier, Christophe / Shechtman, Yoav / Jug, Florian /
    Heilemann, Mike / Jacquemet, Guillaume / Henriques, Ricardo

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 2276

    Abstract: Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to ... ...

    Abstract Deep Learning (DL) methods are powerful analytical tools for microscopy and can outperform conventional image processing pipelines. Despite the enthusiasm and innovations fuelled by DL technology, the need to access powerful and compatible resources to train DL networks leads to an accessibility barrier that novice users often find difficult to overcome. Here, we present ZeroCostDL4Mic, an entry-level platform simplifying DL access by leveraging the free, cloud-based computational resources of Google Colab. ZeroCostDL4Mic allows researchers with no coding expertise to train and apply key DL networks to perform tasks including segmentation (using U-Net and StarDist), object detection (using YOLOv2), denoising (using CARE and Noise2Void), super-resolution microscopy (using Deep-STORM), and image-to-image translation (using Label-free prediction - fnet, pix2pix and CycleGAN). Importantly, we provide suitable quantitative tools for each network to evaluate model performance, allowing model optimisation. We demonstrate the application of the platform to study multiple biological processes.
    MeSH term(s) Animals ; Cell Line, Tumor ; Cloud Computing ; Datasets as Topic ; Deep Learning ; Humans ; Image Processing, Computer-Assisted/methods ; Microscopy/methods ; Primary Cell Culture ; Rats ; Software
    Language English
    Publishing date 2021-04-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-021-22518-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: The effects of different syringe volume, needle size and sample volume on blood gas analysis in syringes washed with heparin.

    Küme, Tuncay / Sişman, Ali Riza / Solak, Ahmet / Tuğlu, Birsen / Cinkooğlu, Burcu / Coker, Canan

    Biochemia medica

    2012  Volume 22, Issue 2, Page(s) 189–201

    Abstract: Introduction: We evaluated the effect of different syringe volume, needle size and sample volume on blood gas analysis in syringes washed with heparin.: Materials and methods: In this multi-step experimental study, percent dilution ratios (PDRs) and ... ...

    Abstract Introduction: We evaluated the effect of different syringe volume, needle size and sample volume on blood gas analysis in syringes washed with heparin.
    Materials and methods: In this multi-step experimental study, percent dilution ratios (PDRs) and final heparin concentrations (FHCs) were calculated by gravimetric method for determining the effect of syringe volume (1, 2, 5 and 10 mL), needle size (20, 21, 22, 25 and 26 G) and sample volume (0.5, 1, 2, 5 and 10 mL). The effect of different PDRs and FHCs on blood gas and electrolyte parameters were determined. The erroneous results from nonstandardized sampling were evaluated according to RiliBAK's TEa.
    Results: The increase of PDRs and FHCs was associated with the decrease of syringe volume, the increase of needle size and the decrease of sample volume: from 2.0% and 100 IU/mL in 10 mL-syringe to 7.0% and 351 IU/mL in 1 mL-syringe; from 4.9% and 245 IU/mL in 26G to 7.6% and 380 IU/mL in 20 G with combined 1 mL syringe; from 2.0% and 100 IU/mL in full-filled sample to 34% and 1675 IU/mL in 0.5 mL suctioned sample into 10 mL-syringe. There was no statistical difference in pH; but the percent decreasing in pCO2,, K+, iCa2+, iMg2+; the percent increasing in pO2 and Na+ were statistical significance compared to samples full-filled in syringes. The all changes in pH and pO2 were acceptable; but the changes in pCO2, Na+, K+ and iCa2+ were unacceptable according to TEa limits except fullfilled-syringes.
    Conclusions: The changes in PDRs and FHCs due nonstandardized sampling in syringe washed with liquid heparin give rise to erroneous test results for pCO2 and electrolytes.
    MeSH term(s) Blood Gas Analysis ; Blood Specimen Collection/methods ; Blood Specimen Collection/standards ; Calibration ; Chemistry Techniques, Analytical ; Diagnostic Errors/prevention & control ; Electrolytes/analysis ; Equipment Design ; Heparin/chemistry ; Humans ; Hydrogen-Ion Concentration ; Needles ; Point-of-Care Systems ; Syringes
    Chemical Substances Electrolytes ; Heparin (9005-49-6)
    Language English
    Publishing date 2012-07-24
    Publishing country Croatia
    Document type Journal Article
    ZDB-ID 1208725-7
    ISSN 1846-7482 ; 1330-0962
    ISSN (online) 1846-7482
    ISSN 1330-0962
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: OME-Zarr: a cloud-optimized bioimaging file format with international community support.

    Moore, Josh / Basurto-Lozada, Daniela / Besson, Sébastien / Bogovic, John / Bragantini, Jordão / Brown, Eva M / Burel, Jean-Marie / Moreno, Xavier Casas / de Medeiros, Gustavo / Diel, Erin E / Gault, David / Ghosh, Satrajit S / Gold, Ilan / Halchenko, Yaroslav O / Hartley, Matthew / Horsfall, Dave / Keller, Mark S / Kittisopikul, Mark / Kovacs, Gabor /
    Yoldaş, Aybüke Küpcü / Kyoda, Koji / de la Villegeorges, Albane le Tournoulx / Li, Tong / Liberali, Prisca / Lindner, Dominik / Linkert, Melissa / Lüthi, Joel / Maitin-Shepard, Jeremy / Manz, Trevor / Marconato, Luca / McCormick, Matthew / Lange, Merlin / Mohamed, Khaled / Moore, William / Norlin, Nils / Ouyang, Wei / Özdemir, Bugra / Palla, Giovanni / Pape, Constantin / Pelkmans, Lucas / Pietzsch, Tobias / Preibisch, Stephan / Prete, Martin / Rzepka, Norman / Samee, Sameeul / Schaub, Nicholas / Sidky, Hythem / Solak, Ahmet Can / Stirling, David R / Striebel, Jonathan / Tischer, Christian / Toloudis, Daniel / Virshup, Isaac / Walczysko, Petr / Watson, Alan M / Weisbart, Erin / Wong, Frances / Yamauchi, Kevin A / Bayraktar, Omer / Cimini, Beth A / Gehlenborg, Nils / Haniffa, Muzlifah / Hotaling, Nathan / Onami, Shuichi / Royer, Loic A / Saalfeld, Stephan / Stegle, Oliver / Theis, Fabian J / Swedlow, Jason R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing ...

    Abstract A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself -- OME-Zarr -- along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.
    Language English
    Publishing date 2023-05-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.17.528834
    Database MEDical Literature Analysis and Retrieval System OnLINE

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