<meta charset="utf8"></head><body>使用 TSAI 加速组织微阵列成像的 MIBI 运行设置

<ol>
	<li>Liu, C. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+Ion+Beam+Imaging:+Insights+into+Pathobiology.">Multiplexed Ion Beam Imaging: Insights into Pathobiology.</a> Annu Rev Pathol. 17, 403-423 (2022).</li><li>Keren, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MIBI-TOF:+A+multiplexed+imaging+platform+relates+cellular+phenotypes+and+tissue+structure.">MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure.</a> Sci Adv. 5 (10), 1-16 (2019).</li><li>Elhanani, O., Keren, L., Angelo, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-Dimensional+Tissue+Profiling+by+Multiplexed+Ion+Beam+Imaging.">High-Dimensional Tissue Profiling by Multiplexed Ion Beam Imaging.</a> Methods Mol Biol. 2386, 147-156 (2022).</li><li>Greenwald, N. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-cell+segmentation+of+tissue+images+with+human-level+performance+using+large-scale+data+annotation+and+deep+learning.">Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning.</a> Nat Biotechnol. 40 (4), 555-565 (2022).</li><li>Risom, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transition+to+invasive+breast+cancer+is+associated+with+progressive+changes+in+the+structure+and+composition+of+tumor+stroma.">Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma.</a> Cell. 185 (2), 299.e18-310.e18 (2022).</li><li>McCaffrey, E. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+immunoregulatory+landscape+of+human+tuberculosis+granulomas.">The immunoregulatory landscape of human tuberculosis granulomas.</a> Nat. Immunol. 23 (2), 318-329 (2022).</li><li>Greenbaum, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+spatially+resolved+timeline+of+the+human+maternal&#8211;fetal+interface.">A spatially resolved timeline of the human maternal&#8211;fetal interface.</a> Nature. 619 (7970), 595-605 (2023).</li><li>Hartmann, F. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+metabolic+profiling+of+human+cytotoxic+T+cells.">Single-cell metabolic profiling of human cytotoxic T cells.</a> Nat Biotechnol. 39 (2), 186-197 (2021).</li><li>Patwa, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplexed+imaging+analysis+of+the+tumor-immune+microenvironment+reveals+predictors+of+outcome+in+triple-negative+breast+cancer.">Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer.</a> Commun Biol. 4 (1), 852 (2021).</li><li>Keren, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Structured+Tumor-Immune+Microenvironment+in+Triple+Negative+Breast+Cancer+Revealed+by+Multiplexed+Ion+Beam+Imaging.">A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.</a> Cell. 174 (6), 1373.e19-1387.e19 (2018).</li><li>Vijayaragavan, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+spatial+proteomic+imaging+for+human+neuropathology.">Single-cell spatial proteomic imaging for human neuropathology.</a> Acta Neuropathol. Commun. 10 (1), 158 (2022).</li><li>. GitHub - angelolab/toffy: Scripts for interacting with and generating data from the commercial MIBIScope. (n.d.) Available from: <a target="_blank" href="https://github.com/angelolab/toffy">https://github.com/angelolab/toffy</a> (2023)</li><li>. HTML Living Standard Available from: <a target="_blank" href="https://html.spec.whatwg.org/multipage">https://html.spec.whatwg.org/multipage</a> (2023)</li><li>. ECMAScript 2022 Language Specification Available from: <a target="_blank" href="https://www.ecma-international.org/publications-and-standards/standards/ecma-262">https://www.ecma-international.org/publications-and-standards/standards/ecma-262</a> (2023)</li><li>. Cascading Style Sheets (CSS) Available from: <a target="_blank" href="https://www.w3.org/Style/CSS/Overview.en.html">https://www.w3.org/Style/CSS/Overview.en.html</a> (2023)</li></ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>MIBI computer</td>
			<td>Ionpath</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MIBIcontrol (software)</td>
			<td>Ionpath</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MIBIscope</td>
			<td>Ionpath</td>
			<td></td>
			<td>Multiplexed Ion Beam Imaging (MIBI) microscope</td>
		</tr>
		<tr>
			<td>MIBIslide</td>
			<td>Ionpath</td>
			<td>567001</td>
			<td>Conductive slide for MIBI</td>
		</tr>
		<tr>
			<td>Tile/SED/Array Interface (TSAI) (software)</td>
			<td></td>
			<td>https://github.com/ag-tsai/mibi_tsai/</td>
			<td></td>
		</tr>
	</tbody>
</table>

rapid setup of tissue microarray and tiled area imaging on the multiplexed ion beam imaging microscope using the tile/sed/array interface 

Multiplexed ion beam imaging (MIBI) is a technique to image 40+ proteins simultaneously on histologic tissue sections at up to 250 nm resolution1,2,3. After a histologic tissue section is stained using antibodies tagged with isotopically pure elemental metals, the MIBI instrument performs secondary ion mass spectrometry to simultaneously quantify all the isotopes - and thus expression of all 40+ antigens - at individual spots on the tissue. Performed across grids of millions of spots, the resulting 40+ plex images of protein expression enable the delineation of cell boundaries and identification of specific cell types while preserving spatial context1,2,3,4. This technique has been used by hundreds of users at roughly 20 sites to study the cellular composition, metabolic profiles, and/or architecture of dozens of tissue types as part of examining the immune response to tumors, tissue inflammation caused by infectious agents, neuropathology of dementia, and immune tolerance in pregnancy5,6,7,8,9,10,11.
A key bottleneck in MIBI instrument operation is setting up fields of view (FOVs) - 200&#160;x 200 &#181;m2 to 800&#160;x 800 &#181;m2 areas of the tissue - for imaging. The MIBI images one FOV at a time, up to 800&#160;x 800 &#181;m2, thus imaging larger areas requires stitching multiple FOVs together. Imaging a tissue microarray (e.g., eight circular tissues in Figure 1A) involves placing multiple FOVs spaced apart. To set up FOVs, the manufacturer interface provides 1) an optical camera image of the slide with a crosshair that roughly corresponds to the specified imaging coordinate (Figure 1A) and 2) a secondary electron detector (SED) image that shows the exact area at the coordinate, reportedly accurate to within 0.1 &#181;m (Figure 1B). First, the user roughly positions a single FOV using the optical image. Because the image resolution is only about 60 &#181;m per pixel, if the placement is off by two pixels (2 pixels&#160;x 60 &#181;m per pixel), a standard 400 &#181;m FOV will be off by 30%. Thus, the user must use the SED image to fine-tune the position - a tedious sequence of a dozen steps involving multiple popup windows, typing coordinates into text boxes, slowly nudging the SED with directional control buttons, and often even writing down coordinates on paper (Supplementary Figure 1). This process must be repeated for each spot of a 100+ core tissue microarray (TMA). Some third-party tools can help with the initial rough positioning12. However, they still require some programming knowledge, and final positioning is still done through the dozen-step process. It is also highly troublesome to position grids of adjacent FOVs, which will be later stitched together into a tiled panoramic image.
Thus, the tile/SED/array Interface (TSAI) was developed with the goal of enabling users to rapidly position large numbers of FOVs using an intuitive, interactive graphical interface. TSAI consists of two main components: 1) A web-based graphical user interface (web UI) for rapidly placing TMA points and tissue tiles, and 2) Integrations into the MIBI user control interface for generating a tiled SED image and adjusting FOV positions. If only using the optical image, many FOVs can be roughly positioned and then quickly adjusted using the FOV navigation/adjustment tools (Figure 2, TSAI, left branch). However, if the SED tiling is performed, FOVs can be accurately positioned on the tiled SED image without needing further adjustments in SED mode (Figure 2, TSAI, right branch). Of general interest to hundreds of current MIBI users, these tools make tiling and TMA positioning very simple even for novices and reduce complex MIBI run setups from several hours to a few dozen minutes.

<meta charset="utf8"></head><body>作者聚焦：介绍用于组织成像中快速视场定位的 Tile/SED/Array 接口

使用 Tile/SED/Array 接口在多路复用离子束成像显微镜上快速构建组织微阵列和平铺面积成像 

Multiplexed ion beam imaging, or MIBI, is a technique to image protein expression in histological tissues across dozens of proteins simultaneously. Using MIBI, researchers can identify, locate, and characterize cells in their native tissue environments. A key bottleneck in MIBI instrument operation is setting up fields of view, or FOVs, for imaging.FOVs are 200 by 200 micron to 800 by 800 micron areas on the slide which users position to cover tissue regions of interest. Positioning FOVs for large contiguous areas of tissue and large tissue microarrays is unwieldy using the manufacturer's interface. We developed the tile/SED/array interface to help users this rapidly position large numbers of FOVs using an intuitive, interactive graphical interface.

Read this Scientific Article Protocol about Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope using the Tile/SED/Array Interface at JoVE.com

Multiplexed ion beam imaging (MIBI) is a next-generation mass spectrometry-based microscopy technique&#160;that generates 40+ plex images of protein ...

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Biology

Rapid Setup of Tissue Microarray and Tiled Area Imaging on the Multiplexed Ion Beam Imaging Microscope Using the Tile/SED/Array Interface 

290 Views.  Stanford University. Multiplexed ion beam imaging, or MIBI, is a technique to image protein expression in histological tissues across dozens of proteins simultaneously. Using MIBI, researchers can identify, locate, and characterize cells in their native tissue environments. A key bottleneck in MIBI instrument operation is setting up fields of view, or FOVs, for imaging.FOVs are 200 by 200 micron to 800 by 800 micron areas on the slide which users position to cover tissue regions of interest. Positioning FO...