MediaWiki API result
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{
"compare": {
"fromid": 1,
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"fromtitle": "Main Page",
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"torevid": 2,
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"totitle": "Main Page/BPHS 4090/microscopy I",
"*": "<tr><td colspan=\"2\" class=\"diff-lineno\" id=\"mw-diff-left-l1\" >Line 1:</td>\n<td colspan=\"2\" class=\"diff-lineno\">Line 1:</td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">'''MediaWiki has been successfully installed.'''</del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><h1>Required Components</h1></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><ol></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Diatom slide</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Stage micrometer slide</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Stained and unstained baboon eye slides</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Fresh onion</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Knife and tweezers</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Toothpick or popsicle sticks</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Blank slides and coverslips</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Syringe of vaseline with pipet tip end</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Distilled water</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Immersion oil</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>Nikon upright microscope and CCD camera</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li>USB stick for transferring data and images for processing and report generation</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"></ol></ins></div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'></td><td class='diff-marker'>\u00a0</td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">Consult </del>the <del class=\"diffchange diffchange-inline\">[http://meta</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.<del class=\"diffchange diffchange-inline\">org/wiki/Help:Contents User's Guide] for information </del>on <del class=\"diffchange diffchange-inline\">using </del>the <del class=\"diffchange diffchange-inline\">wiki software</del>.</div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><h1>Objectives</h1></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>Students will get a refresher on </ins>the <ins class=\"diffchange diffchange-inline\">optical light path of microscopes as well as working with</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">digital acquisition software and data processing</ins>. <ins class=\"diffchange diffchange-inline\">Building off of previous knowledge, the</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">students will explore light contrast modes for unstained samples like darkfield imaging and</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">phase contrast imaging</ins>. <ins class=\"diffchange diffchange-inline\">In the first part of this lab these modes will be compared with standard</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">brightfield illumination </ins>on <ins class=\"diffchange diffchange-inline\">stained and unstained specimens. In </ins>the <ins class=\"diffchange diffchange-inline\">second part darkfield</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">imaging will be used to measure the cytoplasmic streaming rate of spherosomes in living onion</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">cells</ins>.<ins class=\"diffchange diffchange-inline\"></p></ins></div></td></tr>\n<tr><td class='diff-marker'>\u00a0</td><td class='diff-context'></td><td class='diff-marker'>\u00a0</td><td class='diff-context'></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">== Getting started ==</del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><h1>Introduction</h1></ins></div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">* [http:</del>/<del class=\"diffchange diffchange-inline\">/www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Manual</del>:<del class=\"diffchange diffchange-inline\">Configuration_settings Configuration settings list]</del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>Imaging has become a vital tool for researchers in virtually all aspects of modern biophysics.</ins></div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">* [http</del>://<del class=\"diffchange diffchange-inline\">www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Manual:FAQ MediaWiki FAQ]</del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">Recent advances in microscope technology as well as labelling techniques and gene and protein</ins></div></td></tr>\n<tr><td class='diff-marker'>\u2212</td><td class='diff-deletedline'><div><del class=\"diffchange diffchange-inline\">* [https:</del>//<del class=\"diffchange diffchange-inline\">lists</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">mailman/listinfo</del>/<del class=\"diffchange diffchange-inline\">mediawiki-announce MediaWiki release mailing list]</del></div></td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">manipulation methods have led to breakthroughs in our understanding of biological processes.</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">In order to take advantage of these methods you, the biophysicist, need to understand some of</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">the fundamental techniques and concepts in microscopy. You already have experience with</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">microscopes, and this lab will build on that knowledge and get you familiar with more advanced</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">methods as well as working with acquisition software.<</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>The brightfield (transmitted light) imaging mode is something you have already been exposed</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">to. Brightfield imaging mimics the human optical system and is measured in terms of colour and</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">light intensity absorbed by a sample. The contrast method is based off of colour specific</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">absorption of light by the dyes added into the specimen. When working with certain samples,</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">particularly live specimens, the addition of exogenous contrast agents isn\u2019t always feasible as</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">they can potentially interfere with the organism or cells under observation</ins>. <ins class=\"diffchange diffchange-inline\">In this lab we will</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">focus on some specialized microscope techniques to look at unstained samples in a way that lets</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">you observe their morphology without the addition of foreign compounds</ins>. <ins class=\"diffchange diffchange-inline\">The imaging modes</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">you will be using are:<</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><ol></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li><b>Brightfield:<</ins>/<ins class=\"diffchange diffchange-inline\">b> where samples contain little natural contrast and dyes are added to impart</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">artificial colour</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li><b>Darkfield</ins>:<ins class=\"diffchange diffchange-inline\"></b> where photons observed are mostly those that have been scattered by structures</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">within the samples</li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><li><b>Phase Contrast</ins>:<ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">b> where optics will be used to visualize changes in the optical path length of</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">samples<</ins>/<ins class=\"diffchange diffchange-inline\">li></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>A refresher on optical microscopy and imaging theory is included in Appendix 1</ins>. <ins class=\"diffchange diffchange-inline\">Please refer to</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">this section to review some of the fundamental concepts in microscopy. If you feel comfortable</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">with this content you do not have to read through it thoroughly. It has been included as</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">optional background material</ins>.<ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><h2>Brightfield Staining<</ins>/<ins class=\"diffchange diffchange-inline\">h2></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>Most biomedical microscopy specimens contain very little intrinsic contrast when viewed</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">directly with transmitted light. For example, to make specimens such as the tissue sections you</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">are using in this lab easier to visualize, stains and dyes are used. These compounds impart</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">additional contrast and enable discrimination of morphological features based on their</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">differential colour absorption across the visible spectrum.<</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>By far, the most common type of stain used in biological microscopy is Haematoxylin & Eosin</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">(H&E). Haematoxylin stains basophilic chemical structures such as DNA in the nucleus dark</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">purple, while Eosin will stain the cytoplasm and extra-cellular regions a shade of pink. When</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">oxidized, haematoxylin forms a structure called haematein. Haematein is a compound that</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">forms strongly coloured complexes with metal ions, most notably Fe(III) and Al(III), and it is</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">these coloured complexes which give the blue</ins>/<ins class=\"diffchange diffchange-inline\">purple colouring seen in the nuclei of H&E</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">sections</ins>. <ins class=\"diffchange diffchange-inline\">H&E staining allows pathologists to observe the density and shape of nuclei in tissue</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">sections, and is the gold standard in the diagnosis of many types of Cancer</ins>.<ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\"><p>Shown in Figure 1 is a sample of an H&E stained tissue section from a rabbit brain. A low</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">resolution image shows a brain tumour as the dark purple mass, and the zoom view shows the</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">border between tumour and healthy tissue. Note the dark purple staining of the cancerous</ins></div></td></tr>\n<tr><td colspan=\"2\">\u00a0</td><td class='diff-marker'>+</td><td class='diff-addedline'><div><ins class=\"diffchange diffchange-inline\">nuclei, and how densely packed they are.<</ins>/<ins class=\"diffchange diffchange-inline\">p></ins></div></td></tr>\n"
}
}