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Adding videos contributed by Leanne Arakkal ORCID 0000-0001-9189-7172.
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Adding tutorial videos, setting focus map in Leica LAS X Navigator and
sectioning with and without static gun.
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zivy committed Jan 3, 2025
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Expand Up @@ -13,22 +13,27 @@ Leica LAS X Linked Shading: Fluorescence,https://www.youtube.com/watch?v=9l_DmMm
Leica LAS X THUNDER Tutorial,https://www.youtube.com/watch?v=36HqrFyy0fQ,"This video shows how to ""THUNDER"" images in LAS X on-the-fly or post-acquisition with the default settings. (v. 3.7.1 - Widefield). This is only available on THUNDER Imagers.",tutorial,2020,6,9,
Leica LAS X Software Experiment Setup: Z-stack,https://www.youtube.com/watch?v=dTMF01cO7lI,"How to set up a Z-stack in LAS X v 3.3 (widefield). Note: the example in this video was for a data set that was intended for deconvolution, so it goes slightly beyond the focus on either end. The usual recommendation is to stay mostly in focus for all of your Z planes, so that subsequent 2D projections (such as a maximum intensity projection or extended depth of focus projection) will be clearer.",tutorial,2020,6,9,
Automated IBEX multiplex immunohistochemistry using Fluigent's ARIA,https://www.youtube.com/watch?v=mp-gj1O3ntE,"In this webinar, Dr. Colin Chu (UCL Institute of Ophthalmology, UK) presents the integration of the ARIA fluidics device and THUNDER imager developed in the Germain laboratory at the NIH. Additionally, Dr. Chu describes how he extended the automated IBEX method, developed with James Marr, Andrea Radtke, and Ziv Yaniv, to the retina with his team at UCL. Image credits: Stained glass window cover slide and promotional material (Andrea Radtke and Stefan Uderhardt), lymph node IBEX images (Andrea Radtke), jejunum IBEX images (Andrea Radtke and Colin Chu), skin automated IBEX images (Hiroshi Ichise and Andrea Radtke). The original IBEX method and image alignment software was developed by Drs. Andrea Radtke and Ziv Yaniv at the NIH.",general,2024,6,30,0000-0003-2088-8310
Accelerating discovery together: A community approach to multiplexed tissue imaging,https://www.youtube.com/watch?v=GsoJdrszzVc,"<p>
This webinar gives a broad overview of spatial biology techniques with a special emphasis on the iterative bleaching extends multiplexity (IBEX) technique, an open source method for highly multiplexed imaging (65+ parameters). In the webinar, Dr. Radtke describes two communities working to reduce the time, cost, and expertise required to adopt multiplexed antibody-based imaging approaches. The first resource is the IBEX Knowledge-Base, an open, global repository for reagents, protocols, datasets, and software related to IBEX and other spatial biology methods. Here, Dr. Radtke reviews the design, motivation, and utility of the IBEX Knowledge-Base and associated community. The second resource, led by the Human BioMolecular Atlas Program (HuBMAP), involves the publication of community-validated Organ Mapping Antibody Panels (OMAPs).
</p>

<p>
This webinar was initially recorded for the Nature Spatial Biology Conference, October 29th, 2024. Helpful resources mentioned in the talk
<ul>
<li>Reviews on multiplexed tissue imaging: <a href=""https://doi.org/10.1038/s41592-021-01316-y"">https://doi.org/10.1038/s41592-021-01316-y</a>, <a href=""https://doi.org/10.1182/blood.2023020999"">https://doi.org/10.1182/blood.2023020999</a>.
</li>
<li>IBEX: <a href=""https://doi.org/10.1073/pnas.2018488117"">https://doi.org/10.1073/pnas.2018488117</a>, <a href=""https://doi.org/10.1038/s41596-021-00644-9"">https://doi.org/10.1038/s41596-021-00644-9</a>.
</li>
<li>IBEX applications: <a href=""https://doi.org/10.1016/j.ccell.2024.02.001"">https://doi.org/10.1016/j.ccell.2024.02.001</a>, <a href=""https://doi.org/10.1038/s41586-024-07944-6"">https://doi.org/10.1038/s41586-024-07944-6</a>.
</li>
<li>IBEX Knowledge-Base: <a href=""https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/"">https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/</a>, <a href=""https://doi.org/10.5281/zenodo.13122300"">https://doi.org/10.5281/zenodo.13122300</a>.
</li>
<li>OMAPs: <a href=""https://doi.org/10.1038/s41592-023-01846-7"">https://doi.org/10.1038/s41592-023-01846-7</a>, <a href=""https://humanatlas.io/omap"">https://humanatlas.io/omap</a>
</li>
</ul>
</p>",general,2024,12,6,0000-0003-4379-8967
Accelerating discovery together: A community approach to multiplexed tissue imaging,https://www.youtube.com/watch?v=GsoJdrszzVc,"<p>
This webinar gives a broad overview of spatial biology techniques with a special emphasis on the iterative bleaching extends multiplexity (IBEX) technique, an open source method for highly multiplexed imaging (65+ parameters). In the webinar, Dr. Radtke describes two communities working to reduce the time, cost, and expertise required to adopt multiplexed antibody-based imaging approaches. The first resource is the IBEX Knowledge-Base, an open, global repository for reagents, protocols, datasets, and software related to IBEX and other spatial biology methods. Here, Dr. Radtke reviews the design, motivation, and utility of the IBEX Knowledge-Base and associated community. The second resource, led by the Human BioMolecular Atlas Program (HuBMAP), involves the publication of community-validated Organ Mapping Antibody Panels (OMAPs).
</p>

<p>
This webinar was initially recorded for the Nature Spatial Biology Conference, October 29th, 2024. Helpful resources mentioned in the talk
<ul>
<li>Reviews on multiplexed tissue imaging: <a href=""https://doi.org/10.1038/s41592-021-01316-y"">https://doi.org/10.1038/s41592-021-01316-y</a>, <a href=""https://doi.org/10.1182/blood.2023020999"">https://doi.org/10.1182/blood.2023020999</a>.
</li>
<li>IBEX: <a href=""https://doi.org/10.1073/pnas.2018488117"">https://doi.org/10.1073/pnas.2018488117</a>, <a href=""https://doi.org/10.1038/s41596-021-00644-9"">https://doi.org/10.1038/s41596-021-00644-9</a>.
</li>
<li>IBEX applications: <a href=""https://doi.org/10.1016/j.ccell.2024.02.001"">https://doi.org/10.1016/j.ccell.2024.02.001</a>, <a href=""https://doi.org/10.1038/s41586-024-07944-6"">https://doi.org/10.1038/s41586-024-07944-6</a>.
</li>
<li>IBEX Knowledge-Base: <a href=""https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/"">https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/</a>, <a href=""https://doi.org/10.5281/zenodo.13122300"">https://doi.org/10.5281/zenodo.13122300</a>.
</li>
<li>OMAPs: <a href=""https://doi.org/10.1038/s41592-023-01846-7"">https://doi.org/10.1038/s41592-023-01846-7</a>, <a href=""https://humanatlas.io/omap"">https://humanatlas.io/omap</a>
</li>
</ul>
</p>",general,2024,12,6,0000-0003-4379-8967
How to section using the CryoJane Tape-Transfer System,https://www.youtube.com/watch?v=iBThDHb4lrs,A video tutorial on how to section using the CryoJane Tape-Transfer System.,tutorial,2024,12,29,0000-0001-9189-7172
Sectioning with Static Gun,https://www.youtube.com/watch?v=yIpe4iaYNVQ,"The manual IBEX method utilizes a 2-well chambered coverglass to prevent tissue loss from coverslip removal and addition after each imaging round. Static electricity is a common challenge when preparing tissue sections for these chambers. Here, we demonstrate how to use the ZEROSTAT3 anti-static gun to reduce static electricity and successfully prepare tissue sections in a 2-well chambered coverglass. Compare the results of this video to the video titled, <a href=""https://www.youtube.com/watch?v=yIpe4iaYNVQ"">Sectioning without Static Gun</a> for proof that the anti-static gun works!",tutorial,2024,12,29,0000-0001-9189-7172
Sectioning without Static Gun,https://www.youtube.com/watch?v=ClnHRQ0lQq8,"The manual IBEX method utilizes a 2-well chambered coverglass to prevent tissue loss from coverslip removal and addition after each imaging round. Static electricity is a common challenge when preparing tissue sections for these chambers. The tissue section clings to the plastic sides of the coverglass due to static electricity (See 0:44 to 0:53). Compare the results of this video to the video titled, <a href=""https://www.youtube.com/watch?v=yIpe4iaYNVQ"">Sectioning with Static Gun</a> for proof that the anti-static gun works!",tutorial,2024,12,29,0000-0001-9189-7172
Setting focus map in Leica LAS X Navigator for manual IBEX: 1 of 2 videos,https://www.youtube.com/watch?v=wIfh53wqBmM,"First of two videos demonstrating how to create a focus map in LAS X Navigator (LAS X 3.5.5.19976, Leica TCS SP8 X confocal microscope) for pixel-pixel alignment of manual IBEX images. This video (1 of 2) concerns how to create a focus map before acquiring a Cycle 1 image using the Manual IBEX method. The steps detailed in the video titled <a href=""https://www.youtube.com/watch?v=H9W16NenrM8"">Focus Map Set Up After Cycle 1</a> are to be followed after imaging Cycle 1, dye inactivating Cycle 1 antibodies, labeling with Cycle 2 antibodies and before imaging Cycle 2.",tutorial,2024,12,29,0000-0001-9189-7172
Focus Map Set Up After Cycle 1 for manual IBEX: 2 of 2 videos,https://www.youtube.com/watch?v=H9W16NenrM8,"Second of two videos demonstrating how to use a focus map in LAS X Navigator (LAS X 3.5.5.19976, Leica TCS SP8 X confocal microscope) for pixel-pixel alignment of manual IBEX images. This video (2 of 2) concerns how to set up a focus map after acquiring a Cycle 1 image. See video titled, <a href=""https://www.youtube.com/watch?v=wIfh53wqBmM"">Setting focus map in Leica LAS X Navigator for manual IBEX: 1 of 2 videos</a> for details on how to set up a tile scan and focus map for manual IBEX.""",tutorial,2024,12,29,0000-0001-9189-7172

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