Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method Article Swipe

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Quanyou Cai , Lihui Lin , Xinjun Liu , Jiekai Chen ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1101/gr.280532.125

Integration of single-cell and spatial transcriptomes represents a fundamental strategy to enhance spatial data quality. However, existing methods for mapping single-cell data to spatial coordinates struggle with large-scale data sets comprising millions of cells. Here, we introduce Polyomino, an intelligent region-allocation method inspired by the region-of-interest (ROI) concept from image processing. By using gradient descent, Polyomino allocates cells to structured spatial regions that match the most significant biological information, optimizing the integration of data and improving speed and accuracy. Polyomino excels in integrating data even in the presence of various sequencing artifacts, such as cell segmentation errors and imbalanced cell-type representations. Polyomino outperforms state-of-the-art methods by 10 to 1000 times in speed, and it is the only approach capable of integrating data sets containing millions of cells in a single run. As a result, Polyomino uncovers originally hidden gene expression patterns in brain sections and offers new insights into organogenesis and tumor microenvironments, all with exceptional efficiency and accuracy.

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Type: article
Language: en
Landing Page: https://doi.org/10.1101/gr.280532.125
PDF: http://genome.cshlp.org/content/early/2025/10/20/gr.280532.125.full.pdf
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DOI: https://doi.org/10.1101/gr.280532.125

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Title: Polyomino reconstructs spatial transcriptomic profiles with single-cell resolution via a region-allocation method

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Publication year: 2025

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Publication date: 2025-10-22

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Authors: Quanyou Cai, Lihui Lin, Xinjun Liu, Jiekai Chen

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Landing page: https://doi.org/10.1101/gr.280532.125

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abstract_inverted_index.various	89
abstract_inverted_index.However,	15
abstract_inverted_index.approach	117
abstract_inverted_index.descent,	54
abstract_inverted_index.existing	16
abstract_inverted_index.gradient	53
abstract_inverted_index.insights	147
abstract_inverted_index.inspired	42
abstract_inverted_index.millions	31, 124
abstract_inverted_index.patterns	140
abstract_inverted_index.presence	87
abstract_inverted_index.quality.	14
abstract_inverted_index.sections	143
abstract_inverted_index.strategy	9
abstract_inverted_index.struggle	25
abstract_inverted_index.uncovers	135
abstract_inverted_index.Polyomino	55, 79, 101, 134
abstract_inverted_index.accuracy.	78, 158
abstract_inverted_index.allocates	56
abstract_inverted_index.cell-type	99
abstract_inverted_index.improving	75
abstract_inverted_index.introduce	36
abstract_inverted_index.Polyomino,	37
abstract_inverted_index.artifacts,	91
abstract_inverted_index.biological	67
abstract_inverted_index.comprising	30
abstract_inverted_index.containing	123
abstract_inverted_index.efficiency	156
abstract_inverted_index.expression	139
abstract_inverted_index.imbalanced	98
abstract_inverted_index.optimizing	69
abstract_inverted_index.originally	136
abstract_inverted_index.represents	6
abstract_inverted_index.sequencing	90
abstract_inverted_index.structured	59
abstract_inverted_index.Integration	0
abstract_inverted_index.coordinates	24
abstract_inverted_index.exceptional	155
abstract_inverted_index.fundamental	8
abstract_inverted_index.integrating	82, 120
abstract_inverted_index.integration	71
abstract_inverted_index.intelligent	39
abstract_inverted_index.large-scale	27
abstract_inverted_index.outperforms	102
abstract_inverted_index.processing.	50
abstract_inverted_index.significant	66
abstract_inverted_index.single-cell	2, 20
abstract_inverted_index.information,	68
abstract_inverted_index.segmentation	95
abstract_inverted_index.organogenesis	149
abstract_inverted_index.transcriptomes	5
abstract_inverted_index.representations.	100
abstract_inverted_index.state-of-the-art	103
abstract_inverted_index.region-allocation	40
abstract_inverted_index.microenvironments,	152
abstract_inverted_index.region-of-interest	45
cited_by_percentile_year
countries_distinct_count	1
institutions_distinct_count	4
citation_normalized_percentile.value	0.47835684
citation_normalized_percentile.is_in_top_1_percent	False
citation_normalized_percentile.is_in_top_10_percent	False