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伪彩色:通过空间和感知优化的伪彩色探索多通道生物医学图像数据。

psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring.

作者信息

Warchol Simon, Troidl Jakob, Muhlich Jeremy, Krueger Robert, Hoffer John, Lin Tica, Beyer Johanna, Glassman Elena, Sorger Peter K, Pfister Hanspeter

机构信息

Harvard John A. Paulson School Of Engineering And Applied Sciences.

Visual Computing Group, Harvard University.

出版信息

bioRxiv. 2024 Jun 15:2024.04.11.589087. doi: 10.1101/2024.04.11.589087.

Abstract

Over the past century, multichannel fluorescence imaging has been pivotal in myriad scientific breakthroughs by enabling the spatial visualization of proteins within a biological sample. With the shift to digital methods and visualization software, experts can now flexibly pseudocolor and combine image channels, each corresponding to a different protein, to explore their spatial relationships. We thus propose psudo, an interactive system that allows users to create optimal color palettes for multichannel spatial data. In psudo, a novel optimization method generates palettes that maximize the perceptual differences between channels while mitigating confusing color blending in overlapping channels. We integrate this method into a system that allows users to explore multi-channel image data and compare and evaluate color palettes for their data. An interactive lensing approach provides on-demand feedback on channel overlap and a color confusion metric while giving context to the underlying channel values. Color palettes can be applied globally or, using the lens, to local regions of interest. We evaluate our palette optimization approach using three graphical perception tasks in a crowdsourced user study with 150 participants, showing that users are more accurate at discerning and comparing the underlying data using our approach. Additionally, we showcase psudo in a case study exploring the complex immune responses in cancer tissue data with a biologist.

摘要

在过去的一个世纪里,多通道荧光成像通过实现生物样本中蛋白质的空间可视化,在无数科学突破中发挥了关键作用。随着向数字方法和可视化软件的转变,专家们现在可以灵活地对每个对应不同蛋白质的图像通道进行伪彩色处理并组合,以探索它们的空间关系。因此,我们提出了psudo,这是一个交互式系统,允许用户为多通道空间数据创建最佳调色板。在psudo中,一种新颖的优化方法生成的调色板能够在减轻重叠通道中令人困惑的颜色混合的同时,最大化通道之间的感知差异。我们将此方法集成到一个系统中,该系统允许用户探索多通道图像数据,并比较和评估其数据的调色板。一种交互式透镜方法提供了关于通道重叠和颜色混淆度量的按需反馈,同时给出了基础通道值的上下文。调色板可以全局应用,也可以使用透镜应用于局部感兴趣区域。我们在一项有150名参与者的众包用户研究中,使用三个图形感知任务评估了我们的调色板优化方法,结果表明用户使用我们的方法在辨别和比较基础数据时更准确。此外,我们在一个案例研究中与一位生物学家展示了psudo在探索癌症组织数据中的复杂免疫反应方面的应用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fab9/11181440/ed2e0dc11a6a/nihpp-2024.04.11.589087v2-f0001.jpg

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