Paper Citation Record · LEDGER

Spatial Transcriptomics as Images for Large-Scale Pretraining

As of 5 August 2026, this Paper Citation Record lists 32 of 32 outbound references and 0 inbound Pith citation observations for arXiv:2603.13432.

A citation records a reference. It does not transfer a finding from one paper to another.

pith.paper-citation-record.v1
2603.13432 v5

Coverage vector

measured 32 of 32 reference resolution

Typed states for the displayed outbound observations.

Source: paper_references, paper_reference_links, observed 2026-07-14T22:11:16.256377Z

measured 32 of 32 standing notices

One-hop event checks from named stored sources.

Source: scholarly_work_events, retraction_status_cache, observed 2026-08-05T06:32:48.257954+00:00

measured 0 of 0 inbound itemization

Pith citing papers itemized under the disclosed page cap.

Source: paper_references, paper_reference_links

measured 0 of 1 external citation measurements

A source-named dated measurement, never combined with another source.

Source: cited_works

Reference resolution

32 of 32 outbound references displayed

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External citation measurements

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Outbound references

Observation 4d6861e3-b116-45c7-b437-4c82a9dc781d · outbound

This paper cites A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart.Cell, 179(7):1647–1660.e19,.

Spatial Transcriptomics as Images for Large-Scale Pretraining A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart.Cell, 179(7):1647–1660.e19,

Reference 1

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation b4683d4f-aacb-400a-a0d3-b8e3e01d722d · outbound

This paper cites Spatially resolved transcriptomes—next generation tools for tissue exploration.BioEssays, 42:1900221, 2020.

Spatial Transcriptomics as Images for Large-Scale Pretraining Spatially resolved transcriptomes—next generation tools for tissue exploration.BioEssays, 42:1900221, 2020

Reference 2

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation ee6f8adc-62fc-460b-978a-38eb0a3bceb6 · outbound

This paper cites an unresolved cited work.

Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 3

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 148d0fd9-963e-41b8-a7d2-6d3ca67c4927 · outbound

This paper cites Boettiger, Jeffrey R.

Spatial Transcriptomics as Images for Large-Scale Pretraining Boettiger, Jeffrey R

Reference 4

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 69f25cfc-8354-447a-be57-cd491d7fad0f · outbound

This paper cites an unresolved cited work.

Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 5

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation d1ca9a7f-8381-46e1-a7c3-ca74f9ea44a5 · outbound

This paper cites scgpt: Towards building a foundation model for single-cell multi-omics using genera- tive ai.bioRxiv, 2023.

Spatial Transcriptomics as Images for Large-Scale Pretraining scgpt: Towards building a foundation model for single-cell multi-omics using genera- tive ai.bioRxiv, 2023

Reference 6

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 5bfd8d18-73e7-4bfa-93d4-dc53f6df8211 · outbound

This paper cites Deciphering spatial do- mains from spatially resolved transcriptomics with an adap- tive graph attention auto-encoder.Nature Communications, 13(1), 2022.

Spatial Transcriptomics as Images for Large-Scale Pretraining Deciphering spatial do- mains from spatially resolved transcriptomics with an adap- tive graph attention auto-encoder.Nature Communications, 13(1), 2022

Reference 7

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 1b0403ee-f740-42d7-8241-a97a34e9eeee · outbound

This paper cites An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale.

Spatial Transcriptomics as Images for Large-Scale Pretraining An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale

Reference 8

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation bb972584-20cd-4a4c-a4e3-4dbe64c6958b · outbound

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Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 9

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 8926dfed-60cd-4408-83ab-bbdd399890f4 · outbound

This paper cites Girshick.

Spatial Transcriptomics as Images for Large-Scale Pretraining Girshick

Reference 10

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 8f3e39e1-0621-43b7-8904-bdcff6b048c9 · outbound

This paper cites Gottscho, Florian Wagner, Stephen R.

Spatial Transcriptomics as Images for Large-Scale Pretraining Gottscho, Florian Wagner, Stephen R

Reference 11

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 144d896f-f44b-435d-9a0a-6c848f3fd115 · outbound

This paper cites Enhanc- ing spatial domain detection in spatial transcriptomics with ensdd.Communications Biology, 7(1), 2024.

Spatial Transcriptomics as Images for Large-Scale Pretraining Enhanc- ing spatial domain detection in spatial transcriptomics with ensdd.Communications Biology, 7(1), 2024

Reference 12

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation c202c578-5dca-4f36-b918-9896263504f3 · outbound

This paper cites ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics.

Spatial Transcriptomics as Images for Large-Scale Pretraining ST-Align: A Multimodal Foundation Model for Image-Gene Alignment in Spatial Transcriptomics

Reference 13

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation c1b9a8ef-2322-4de2-9191-7d1a865dcf47 · outbound

This paper cites Joint cell segmentation and cell type annotation for spatial transcriptomics.Molecu- lar Systems Biology, 17(6), 2021.

Spatial Transcriptomics as Images for Large-Scale Pretraining Joint cell segmentation and cell type annotation for spatial transcriptomics.Molecu- lar Systems Biology, 17(6), 2021

Reference 14

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 452bc434-8437-4d71-9a7b-a5208117c471 · outbound

This paper cites Spatially informed clustering, integration, and de- convolution of spatial transcriptomics with graphst.Nature Communications, 14(1), 2023.

Spatial Transcriptomics as Images for Large-Scale Pretraining Spatially informed clustering, integration, and de- convolution of spatial transcriptomics with graphst.Nature Communications, 14(1), 2023

Reference 15

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation bbd7907e-f6f4-4236-a6d4-21f61fb717d1 · outbound

This paper cites an unresolved cited work.

Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 16

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 2bd11406-c3c0-4590-9a0c-9228567eeb3d · outbound

This paper cites Spatiotemporal dy- namics of molecular pathology in amyotrophic lateral scle- rosis.Science, 364(6435):89–93, 2019.

Spatial Transcriptomics as Images for Large-Scale Pretraining Spatiotemporal dy- namics of molecular pathology in amyotrophic lateral scle- rosis.Science, 364(6435):89–93, 2019

Reference 17

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation c312605f-2d4b-490c-8acb-0ebd56c13b40 · outbound

This paper cites Method of the year: spatially resolved tran- scriptomics.Nature Methods, 18(1):9–14, 2021.

Spatial Transcriptomics as Images for Large-Scale Pretraining Method of the year: spatially resolved tran- scriptomics.Nature Methods, 18(1):9–14, 2021

Reference 18

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation bd1ef0cd-8807-42d7-93b4-31d1299d1106 · outbound

This paper cites Transcriptome-scale spatial gene expres- sion in the human dorsolateral prefrontal cortex.Nature neu- roscience, 24(3):425–436, 2021.

Spatial Transcriptomics as Images for Large-Scale Pretraining Transcriptome-scale spatial gene expres- sion in the human dorsolateral prefrontal cortex.Nature neu- roscience, 24(3):425–436, 2021

Reference 19

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation c2ea514e-127c-4caa-8400-c4a80ffcab6e · outbound

This paper cites Miller, Jean Fan, and Daniel Jacob Tward.

Spatial Transcriptomics as Images for Large-Scale Pretraining Miller, Jean Fan, and Daniel Jacob Tward

Reference 20

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 5548f6f8-ff31-45ba-84a7-ae70a384e1bd · outbound

This paper cites Moffitt, Dhananjay Bambah-Mukku, Stephen W.

Spatial Transcriptomics as Images for Large-Scale Pretraining Moffitt, Dhananjay Bambah-Mukku, Stephen W

Reference 21

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation f6fdf245-ace9-4c76-a72f-a6bf86f8866d · outbound

This paper cites St ˚ahl, Fredrik Salm ´en, Sanja Vickovic, Anna Lundmark, Jos ´e Fern ´andez Navarro, Jens Magnusson, Ste- fania Giacomello, Michaela Asp, Jakub O.

Spatial Transcriptomics as Images for Large-Scale Pretraining St ˚ahl, Fredrik Salm ´en, Sanja Vickovic, Anna Lundmark, Jos ´e Fern ´andez Navarro, Jens Magnusson, Ste- fania Giacomello, Michaela Asp, Jakub O

Reference 22

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 6baab8d4-7d41-4cac-8ba1-ce90f2bc7bc2 · outbound

This paper cites an unresolved cited work.

Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 23

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 7606e5e4-b9ff-4721-9939-c7b1825403ef · outbound

This paper cites Integrating spatial and single-cell transcriptomics data using deep gen- erative models with spatialscope.Nature Communications, 14(1), 2023.

Spatial Transcriptomics as Images for Large-Scale Pretraining Integrating spatial and single-cell transcriptomics data using deep gen- erative models with spatialscope.Nature Communications, 14(1), 2023

Reference 24

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation bbc92aa7-be36-4abc-bb52-d3f461b59691 · outbound

This paper cites scgpt-spatial: Continual pretraining of single-cell foundation model for spatial transcriptomics.bioRxiv, pages 2025–02, 2025.

Spatial Transcriptomics as Images for Large-Scale Pretraining scgpt-spatial: Continual pretraining of single-cell foundation model for spatial transcriptomics.bioRxiv, pages 2025–02, 2025

Reference 25

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation f6bd6f18-f397-4d53-ae3e-2dfa8272003e · outbound

This paper cites Construction of a 3d whole organ- ism spatial atlas by joint modelling of multiple slices with deep neural networks.Nature Machine Intelligence, 5(11): 1200–1213, 2023.

Spatial Transcriptomics as Images for Large-Scale Pretraining Construction of a 3d whole organ- ism spatial atlas by joint modelling of multiple slices with deep neural networks.Nature Machine Intelligence, 5(11): 1200–1213, 2023

Reference 26

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 01c1a335-fe57-4d11-a7eb-b191b5946e0f · outbound

This paper cites Fmh2st: foundation model-based spatial transcriptomics generation from histological images.

Spatial Transcriptomics as Images for Large-Scale Pretraining Fmh2st: foundation model-based spatial transcriptomics generation from histological images

Reference 27

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation e8bc53f5-3c0c-4e61-a58f-5b5b89add90c · outbound

This paper cites Spatial transcriptomics analysis of gene expression pre- diction using exemplar guided graph neural network.Pattern Recognition, 145:109966, 2024.

Spatial Transcriptomics as Images for Large-Scale Pretraining Spatial transcriptomics analysis of gene expression pre- diction using exemplar guided graph neural network.Pattern Recognition, 145:109966, 2024

Reference 28

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 55d65bf4-330c-40b2-b043-d4cf89935b4a · outbound

This paper cites Ritchie, Xiaodong Liu, and Luyi Tian.

Spatial Transcriptomics as Images for Large-Scale Pretraining Ritchie, Xiaodong Liu, and Luyi Tian

Reference 29

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 4bbb9c6d-25f3-494b-9744-e42d1daaa6a4 · outbound

This paper cites SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics.

Spatial Transcriptomics as Images for Large-Scale Pretraining SToFM: a Multi-scale Foundation Model for Spatial Transcriptomics

Reference 30

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Observation 829c24a4-dfd7-4c9c-a593-492e10078b6f · outbound

This paper cites an unresolved cited work.

Spatial Transcriptomics as Images for Large-Scale Pretraining Unresolved cited work

Reference 31

Resolution: verified exact; doi, observed 2026-07-14T22:20:48.281865Z

Source-reported events for the cited work

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Observation fc24526b-4fe1-4d10-bc51-f0da965fcc7e · outbound

This paper cites Uni-mol: A universal 3d molecular representation learning framework.

Spatial Transcriptomics as Images for Large-Scale Pretraining Uni-mol: A universal 3d molecular representation learning framework

Reference 32

Resolution: unresolved; no resolver link, observed 2026-07-14T22:11:16.256377Z

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Pith citing papers

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