TITLE: Online microscopy and histology resources
AUTHORS: Zbigniew Mikulski

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">There is a wealth of microscopy-related information online. This document lists the ones we know and like. Click on the document tab to see the list!</div><div class = "text-block">Last update: 2018-12-28  </div></div>

[STEPS]
?. Microscopy theory and practice:iBiology Microscopy Coursehttps://www.ibiology.org/ibioeducation/taking-courses/ibiology-microscopy-course.htmlFourier transformation explained by 3Blue1Brownhttps://www.youtube.com/watch?v=spUNpyF58BYVendor websites with lots of information about microscopyhttps://www.microscopyu.com/http://zeiss-campus.magnet.fsu.edu/https://www.leica-microsystems.com/science-lab/
Spectra viewers http://www.nightsea.com/sfa-sharing/fluorescence-spectra-viewers/Porweful spectra database of fluorescent proteins and probes by Talley Lamberthttps://www.fpbase.org/
Image analysis:Quantifying microscopy images: top 10 tips for image acquisition by Anne Carpenterhttps://blog.cellprofiler.org/2017/06/15/quantifying-microscopy-images-top-10-tips-for-image-acquisition/Analyzing fluorescence microscopy images with ImageJ by Pete Bankhead
https://petebankhead.gitbooks.io/imagej-intro/content/Image analysis forum for ImageJ, Fiji, CellProfiler, KNIME, Icy, Ilastik, scikit-image, and friendshttps://forum.image.scImage analysis forum for QuPathhttps://groups.google.com/forum/#!forum/qupath-usersQuPath tutorialshttps://www.youtube.com/channel/UCqepVnS1QsB7B8nBA9T91EQ/playlistsFiji manual with tutorials by Cameron J. Nowellhttps://cloudstor.aarnet.edu.au/plus/index.php/s/bxRU7kkoj2rIjCh#pdfviewer - manualhttps://cloudstor.aarnet.edu.au/plus/index.php/s/xdwcNFp0kafaNNN - tutorial dataImmunolabeling:Search for well-referenced antibodies https://www.citeab.com/Open access, online antibody tool https://www.antibodypedia.comMachine learning-based antibody search https://www.benchsci.com/Constantly improving panel of validated human antibodies used in clinical trials http://www.nordiqc.org/Antibody performance following fixationhttps://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-analysis-learning-center/cell-analysis-resource-library/ebioscience-resources/antibody-fixation-considerations.htmlLearn more about tissue markers with Protein Atlas https://www.proteinatlas.org/humanproteome/tissue+specificCell-type speciifc markershttp://www.antibodybeyond.com/reviews/cell-marker-reviews.htmGeneral cell and tissue staining protocolshttps://www.cellsignal.com/contents/resources/protocols/resources-protocolsHistology:Excellent guide on proper murine tissue trimminghttps://reni.item.fraunhofer.de/reni/trimming/Great explanation of HE stain optimizationhttps://www.youtube.com/watch?v=n8VeoXDBDyAHistology of a normal human lymph node (+IHC) https://www.youtube.com/watch?v=RHFzxY4ZeYkNormal skin histologyhttps://www.youtube.com/watch?v=yQQ2Dmz42VsImmunohistochemistry in normal skinhttps://www.youtube.com/watch?v=rNbWCTNUqughttps://www.youtube.com/watch?v=4EmIkhO10uwMedical School Pathology by John R. Minarcik, MDhttps://www.youtube.com/watch?v=SK89_DNoA5Q&list=PL3oAYNQ024sijkTwlmK4MIiyV1Nmv2xZX&index=1Online course - Histology: Using Microscopy to Study Anatomy and Identify DiseaseStart dates 7 January 2019 and 15 July 2019https://www.futurelearn.com/courses/histologyA practical guide to the histology of the mousehttp://www.wiley.com/WileyCDA/WileyTitle/productCd-1119941202.htmlData analysis and visualization:Statistics for biologistshttps://www.nature.com/collections/qghhqmMake a difference: the alternative for p-valueshttp://thenode.biologists.com/quantification-of-differences-as-alternative-for-p-values/research/Plots of data by Marten Postma and Joachim Goedharthttps://huygens.science.uva.nl/PlotsOfData/Getting Started in R by Saghir Basjir and Dirk Eddelbuettelhttps://github.com/eddelbuettel/gsir-teColour schemes and templates, color-blind friendly - excellent resource by Paul Tolhttps://personal.sron.nl/~pault/
Tools:Handbrake - open source video transcoderhttps://handbrake.fr/downloads.phpXnView - free photo viewer, image resizer, batch converterhttps://www.xnview.comVLC media player - open source video playerhttps://www.videolan.org/vlc/index.html