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1 | Helpful Online Resources: | |||||||||||||||||||||||||
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3 | FocalPlane | https://focalplane.biologists.com/ | The new microscopy community site hosted by Journal of Cell Science at The Company of Biologists. We have created this space for you – microscopists, biologists, developers – to share information, connect, interact or just browse the content. | |||||||||||||||||||||||
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5 | COVID-19 Related: | |||||||||||||||||||||||||
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7 | COVID-19 data repository | https://covid19-data.nist.gov | The data in this repository provides direct access to features within the CORD-19 dataset so that researchers can interactively browse and search through the dataset, using keywords, authors, or institutions. AI researchers can directly query the data, which includes both relevant keywords and the full text of the articles. | |||||||||||||||||||||||
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9 | Introduction to Imaging/Fluorescence: | |||||||||||||||||||||||||
10 | Title | Link | Description | |||||||||||||||||||||||
11 | Molecular Expression's optical microscopy primer | https://micro.magnet.fsu.edu/primer/index.html | Introduction to Optical Microscopy,
Digital Imaging, and Photomicrography | |||||||||||||||||||||||
12 | Nikon MicroscopyU: The Source for Microscopy Education | https://www.microscopyu.com/ | Resources for microscopy education with interactive tutorials and articles. | |||||||||||||||||||||||
13 | iBiology: Light Microscopy Series | ibiology.org | iBiology offers online biology courses for early career scientists, biology students and educators. | |||||||||||||||||||||||
14 | MYSCOPE: Microscopy Training | https://myscope.training/ | Developed to provide an online learning environment for those who want to learn about microscopy | |||||||||||||||||||||||
15 | CYTO-U | http://cytou.org/store/provider/provider09.php | ISAC’s online portal for on-demand, peer-reviewed cytometry education, on this site you will have access to multi-module courses, recorded sessions from the CYTO conference, and a regular webinar series. | |||||||||||||||||||||||
16 | QBI Society: Keynote Talks | https://www.quantitativebioimaging.com/ | 2019 Quantitative BioImaging conference (Rennes, France) Keynote Lectures | |||||||||||||||||||||||
17 | MicroCourses: Harvard Medical School Nikon Imaging Centre | https://www.youtube.com/microcourses? | MicroCourses YouTube Channel with instructional videos by Jennifer Waters and Team at Harvard | |||||||||||||||||||||||
18 | Single Molecule Localization Microscopy Principles Lecture | https://figshare.com/articles/Single_Molecule_Localization_Microscopy_Principles_Lecture/11955666 | Lecture on Single Molecule Localization Microscopy principles | |||||||||||||||||||||||
19 | OMX Training Course: Training the Trainer | https://micronoxford.com/omx-training-course | This course is aimed at facility staff working with the DeltaVision OMX 3D structured illumination microscope (3D-SIM). The hands-on course covered a whole range of topics, theory, instrument design and details, calibration, sample preparation, reconstructions and data quality checks. | |||||||||||||||||||||||
20 | Micron Oxford Advanced Microscopy Course | https://micronoxford.com/micron-microscopy-course-1 | The course introduces core principles of brightfield and fluorescence microscopy, biological applications of different imaging approaches and super-resolution techniques. | |||||||||||||||||||||||
21 | Royal Microscopical Society: Online Microscopy Talks | https://www.rms.org.uk/study-read/news-listing-page/online-microscopy-talks-list.html | A list of online imaging opportunities (recorded talks, lecture material, livestreams, etc) | |||||||||||||||||||||||
22 | Imaging & Microscopy Online Edition | https://analyticalscience.wiley.com/do/10.1002/was.00060005 | Magazine that provides readers with thought-provoking and relevant information on developments and trends in microscopy methods in the Life Sciences and Material Sciences | |||||||||||||||||||||||
23 | QuPath Documentation | https://qupath.readthedocs.io/en/latest/ | QuPath Introduction | |||||||||||||||||||||||
24 | QuPath: From Samples to Knowledge Course (La Jolla Microscopy Institute) | https://docs.google.com/document/d/1NYESyNwIYzxYc6Ww4QJLn2tBGs8LYHtewewQ3JexynM/edit | QuPath Instructions from workshop at the La Jolla Microscopy Institute | |||||||||||||||||||||||
25 | https://www.youtube.com/playlist?list=PLlGXRBscPbCD89fRULm4peopF57qugciN | QuPath Workshop recordings on QuPath open source software for bioimage analysis and digital pathology. Files available at: tinycc./filestograb | ||||||||||||||||||||||||
26 | From sample preparation to image analysis course | https://ki.se/en/bionut/microscopy-course | From Sylvie Le Guyader, Live Cell Imaging Facility Manager. Karolinska Institutet- Bionut yearly microscopy course | |||||||||||||||||||||||
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29 | Imaging/Fluorescence Analysis Resources: | |||||||||||||||||||||||||
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31 | Beginner's Guide to Colouring Electron Microscope Images | https://www.youtube.com/watch?v=7vA8sAvPIaA&feature=youtu.be | Beginner's Guide to Colouring Electron Microscope Images by Dr Jenny Whiting | |||||||||||||||||||||||
32 | Huygens Imaging Academy | https://svi.nl/Huygens-imaging-academy | The Huygens Imaging Academy is a public knowledge resource on 3D microscopy, image restoration (Deconvolution), Visualization and Analysis. In addition it serves as a support medium for users of SVI's Huygens Software. | |||||||||||||||||||||||
33 | FIJI/ImageJ Image Processing and Analysis Workshop | https://aicjanelia.wixsite.com/fiji | Materials from workshop (Teng-Leong Chew, Janelia) | |||||||||||||||||||||||
34 | NIH ImageJ tutorials | https://imagej.nih.gov/ij/docs/examples/index.html | ImageJ tutorials and examples. | |||||||||||||||||||||||
35 | NIH Lectures: Bioimage Analysis with FIJI | https://www.youtube.com/channel/UC-hlwQ9Q4GS3rtv2EwSStAQ | YouTube videos of lectures | |||||||||||||||||||||||
36 | Image Analysis with FIJI | http://pcwww.liv.ac.uk/~cci/reveal_ia/ImageAnalysisWithFiji.html | Dave Mason's online workshop using Fiji for image analysis | |||||||||||||||||||||||
37 | Image.sc | https://forum.image.sc/ | Scentific Image Community Forum (particularly for ImageJ, CellProfiler, OME, OpenSPIM, QuPath, NEUBIAS, ImJoy, CLIJ, napari, etc.) | |||||||||||||||||||||||
38 | Microlist | https://forum.microlist.org/ | Microforum’s focus is hardware, acquisition, and specimen-related aspects of scientific imaging. | |||||||||||||||||||||||
39 | Python for Microscopists | https://www.youtube.com/playlist?list=PLZsOBAyNTZwYHBIlu_PUO19M7aHMgwBJr&feature=share | Python tutorials for microscopists with no coding skills | |||||||||||||||||||||||
40 | Introduction to Data Science/Analysis | rafalab.github.io | Teaching data sicence, biostats and bioinformatics | |||||||||||||||||||||||
41 | Materials for Unix, R, Python, etc. | https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources#general | Unix, R and Python tools for genomics and data science | |||||||||||||||||||||||
42 | Introduction to Machine Learning (I2ML) | https://compstat-lmu.github.io/lecture_i2ml/index.html | Introduction to Machine Learning | |||||||||||||||||||||||
43 | Cell Profiler Tutorial | https://www.youtube.com/watch?v=w8dXR4749do&feature=youtu.be | Center for Open Bioimage Analysis | |||||||||||||||||||||||
44 | Imaris Tutorials | https://imaris.oxinst.com/tutorials | Imaris tutorials on image analysis and visualization | |||||||||||||||||||||||
45 | An Introduction to R (Course) | https://alexd106.github.io/intro2R/ | Introduction to R, an interactive environment for statistical computing | |||||||||||||||||||||||
46 | IAFIG-RMS Python for Bioimage Analysis Course | https://github.com/IAFIG-RMS/Python-for-Bioimage-Analysis | IAFIG-RMS Python for Bioimage Analysis Course (designed for one week, with lectures and exercises) | |||||||||||||||||||||||
47 | Python for Beginners Course | https://github.com/ChasNelson1990/python-zero-to-hero-beginners-course | Python 'zero to hero' beginners course (self-taught course 12+ hours) | |||||||||||||||||||||||
48 | iLastik Tutorials | https://www.youtube.com/playlist?list=PLeM_d8ZXiMCNXtVFvwAW23yXfTDsGFk5t | iLastik tutorials on YouTube focused on bioimage analysis. | |||||||||||||||||||||||
49 | Python Bioimage Analysis Course and Support | https://forum.image.sc/t/python-bioimage-analysis-course-and-support/36060?u=chasnelson | Materials from the training course at Cambridge University in December. Support is available on the image.sc forum by tagging your question with #BAPython and tutors for the course will respond to your questions. | |||||||||||||||||||||||
50 | NEUBIAS Academy | http://eubias.org/NEUBIAS/training-schools/neubias-academy-home/ | A series of live online courses on free image analysis platforms including Fiji/ImageJ, Icy, and QuPath. See schedule and register with link for offerings throughout April. | |||||||||||||||||||||||
51 | iBiology Bioimage Analysis course | https://www.youtube.com/playlist?list=PL5ESQNfM5lc5e8v2PlbMdlFVMAODhIgh6 | Lecture Material from course | |||||||||||||||||||||||
52 | Aivia Web | https://www.drvtechnologies.com/aivia-web | Aivia Web provides a simple web-based interface that allows you to access Aivia on a high-performance computer and connect to your data remotely so you can continue your work. From now until May 31, 2020, you can get complimentary access to the pre-release version of Aivia Web. Access is limited to registered users by reservation only. | |||||||||||||||||||||||
53 | Aivia Community - Free 2D/3D/4D Image Visualization Tool and Video Generator | https://www.drvtechnologies.com/aivia-community | Aivia Community - Free 2D/3D/4D Image Visualization Tool and Video Generator | |||||||||||||||||||||||
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55 | Tools Related to Imaging/Fluorescence: | |||||||||||||||||||||||||
56 | Link | Description | ||||||||||||||||||||||||
57 | FPbase | https://www.fpbase.org/ | The fluorescent protein database. | |||||||||||||||||||||||
58 | BenchSci | https://www.benchsci.com/ | BenchSci's online curated published antibody database. | |||||||||||||||||||||||
59 | Bitesize Bio | https://bitesizebio.com/ | Bitesize Bio is an online search tool that allows you to focus in on microscopy news and techniques. | |||||||||||||||||||||||
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61 | Additional Resources: | |||||||||||||||||||||||||
62 | Nyquist Calculator | https://svi.nl/NyquistCalculator | ||||||||||||||||||||||||
63 | Image Size Calculator | https://svi.nl/ImageSizeCalculator | ||||||||||||||||||||||||
64 | SEM/FIB services | https://microscopy.info.yorku.ca/about/ | SEM/FIB services are available for research/industry operating under Ontario Emergency Act | |||||||||||||||||||||||
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