Dataset Open Access

The spatio-temporal landscape of lung pathology in SARS-CoV-2 infection - processed data

Rendeiro, Andre Figueiredo; Ravichandran, Hiranmayi; Bram, Yaron; Steven Salvatore; Borczuk, Alain; Elemento, Olivier; Schwartz, Robert Edward

Recent studies have provided insights into the pathology and immune response to coronavirus disease 2019 (COVID-19). However thorough interrogation of the interplay between infected cells and the immune system at sites of infection is still lacking. Here we use high parameter imaging mass cytometry targeting the expression of 36 proteins, to investigate at single cell resolution, the cellular composition and spatial architecture of the human lung under infection from various pathogens, including SARS-CoV-2. Spatially resolved, single-cell data unravels the disordered structure of the lung along with extensive immune infiltration upon infection. While lymphopenia is common in some infections, neutrophil and macrophage infiltration are hallmarks of pneumonia and COVID-19, respectively. We provide evidence that SARS-CoV-2 infects predominantly alveolar epithelial cells; induces a localized hyper-inflammatory cell state culminating in damage to the lung tissue. By leveraging the temporal range of COVID-19 patient death in relation to the time of symptom onset, we observe increased macrophage extravasation, mesenchymal cells, and fibroblasts abundance concomitant with increased proximity between these cell types as the disease progresses, possibly as an attempt to repair the damaged lung tissue. This spatially resolved single-cell data allowed us to develop a biologically interpretable landscape of lung pathology from a structural, immunological and clinical standpoint. This spatial single-cell landscape enabled the pathophysiological characterization of the human lung from its macroscopic presentation to the single-cell, providing an important basis for the understanding of COVID-19 and lung pathology in general.

We make available binary masks delineating the position of cells in imaging mass cytometry data for all 23 samples, totaling 237 regions of lung tissue. In addition, a h5ad file with intensity values for all single-cells and their classification in clusters and meta-clusters is also available. Companion deposit to https://doi.org/10.5281/zenodo.4110560
Files (1.0 GB)
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3.4 MB Download
processed/20200708_COVID_21_LATE/tiffs/20200708_COVID_21_LATE-11_full_mask.tiff
md5:fdb852ae3463653aa025d1071978adeb
3.4 MB Download
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md5:637fe7c4129c890c9c3e116ec7c61014
2.0 MB Download
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md5:9f0fbc25d72c201f7249954fce4c7fc1
2.0 MB Download
processed/20200708_COVID_21_LATE/tiffs/20200708_COVID_21_LATE-14_full_mask.tiff
md5:a124d4a5dc20483dfe3f1c5a70b11197
2.0 MB Download
processed/20200708_COVID_21_LATE/tiffs/20200708_COVID_21_LATE-15_full_mask.tiff
md5:456c5ee97a076a969dde806ed322806f
10.1 MB Download
processed/20200708_COVID_21_LATE/tiffs/20200708_COVID_21_LATE-16_full_mask.tiff
md5:59dcef0f70a1871109df129a8cd017a0
2.9 MB Download
processed/20200708_COVID_21_LATE/tiffs/20200708_COVID_21_LATE-17_full_mask.tiff
md5:b606d9a2c6f27d43023c3bdba2814ab6
7.2 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-01_full_mask.tiff
md5:b8b044097e21ab2b715240f5907d6365
2.0 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-02_full_mask.tiff
md5:543f06134f1ebcadba569bfa5c81c86b
2.0 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-03_full_mask.tiff
md5:51d0f759c2ce769317a34810e8a3210e
2.0 MB Download
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md5:0a1f6f4e5a16931c3d10fe8169518ac1
2.0 MB Download
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md5:3e8d83d3f6d75617a7e66387cc2ab63e
2.0 MB Download
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md5:ec822c2ed7f2915ac8396c8cc99768a7
2.0 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-07_full_mask.tiff
md5:9de373ec0a4994e64e757d48174d54c8
2.0 MB Download
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md5:20a3d9c157a316ea160352221c072e83
4.5 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-09_full_mask.tiff
md5:c831977e140a24dc37979ffa758af4f2
2.1 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-10_full_mask.tiff
md5:2d842ba3c5e694bc5b16b1137cd2b739
2.0 MB Download
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md5:c6a4c5014f1594e1ebe61bd0941e3c95
1.4 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-12_full_mask.tiff
md5:88787292a7b0a1a49a41b608d51d5f9b
1.4 MB Download
processed/20200713_COVID_3_EARLY/tiffs/20200713_COVID_3_EARLY-13_full_mask.tiff
md5:e9ae98e844742640475efd061ddb1c22
2.0 MB Download
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md5:94d5c069c6964426b3c6b8cf8cf2a3d5
1.6 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-01_full_mask.tiff
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4.5 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-02_full_mask.tiff
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4.5 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-03_full_mask.tiff
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4.5 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-04_full_mask.tiff
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2.9 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-05_full_mask.tiff
md5:065147c307aebb2eacb47e1af3ec3325
6.8 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-06_full_mask.tiff
md5:6b8aec603bb9bed030a4826f7fe9c3e1
3.9 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-07_full_mask.tiff
md5:28ddede01dccf06e06412148beeaaba6
5.4 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-08_full_mask.tiff
md5:eff3a9cf45b187272001796e4271454e
4.5 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-09_full_mask.tiff
md5:d0d94676e23c34c3e15233adcedd7fa1
4.5 MB Download
processed/20200714_FLU_205/tiffs/20200714_FLU_205-10_full_mask.tiff
md5:1eb9a4879053a636713036fde9cd0036
5.4 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-01_full_mask.tiff
md5:dcecc7448baf20f374a94fc3a1db65cc
2.0 MB Download
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md5:9ea81c62a98630cac06136a1af401d71
2.0 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-03_full_mask.tiff
md5:208188ef6580e15cbac9b77572b2146d
5.9 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-04_full_mask.tiff
md5:71693667695345feea7b217bc8d3066e
2.8 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-05_full_mask.tiff
md5:a06415c89024817ec8520561b76c5de6
4.5 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-06_full_mask.tiff
md5:0ad3721b92ed24910364245232452221
5.0 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-07_full_mask.tiff
md5:7f96ef00044d1e9468ef576758033f39
3.6 MB Download
processed/20200716_COVID_1_EARLY/tiffs/20200716_COVID_1_EARLY-08_full_mask.tiff
md5:d12463647b3a9f883c6aff68dd20b859
3.4 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-01_full_mask.tiff
md5:b5c35a927411029ddabcd152046fdbac
4.5 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-02_full_mask.tiff
md5:c959d87fd5302eca8ebf86a90b453d45
2.9 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-03_full_mask.tiff
md5:a5e764f2db6b49579cac780f99845f64
1.8 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-04_full_mask.tiff
md5:e5eeed8c2622cc7a420034a0dfa92de5
4.5 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-05_full_mask.tiff
md5:3882355a24008fbb4d24135ef93ba354
3.4 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-06_full_mask.tiff
md5:5fa2655fbfe0c62b857e1aa356f19a16
980.3 kB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-07_full_mask.tiff
md5:676528b8414c53fabcf0f788f8ee1e89
4.5 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-08_full_mask.tiff
md5:a0c7fe07eb359fe25a1c8bbdb68cf0b4
2.0 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-09_full_mask.tiff
md5:46a837d937a7dbe9bb5e0b4d7cabcf0d
1.6 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-10_full_mask.tiff
md5:97b71ce335380cbedb70de9350ddc45d
2.0 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-11_full_mask.tiff
md5:dd7d6b68c905aaea3e24789cee96c279
1.3 MB Download
processed/20200721_COVID_30_LATE_RUN2/tiffs/20200721_COVID_30_LATE_RUN2-12_full_mask.tiff
md5:aa0ca300cabbfa35aa52687ea068b81f
1.1 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-01_full_mask.tiff
md5:3069d1232367e352d798f737252855e3
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-02_full_mask.tiff
md5:f84b8b4503d68ac1537bf88b3bdb302e
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-03_full_mask.tiff
md5:66413a6efbd86acb359ab5da4e4d4424
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-04_full_mask.tiff
md5:52f8201e355cada39c6ba29b78dc5a2b
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-05_full_mask.tiff
md5:c7cf786049215a3daf91340cda379cee
980.3 kB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-06_full_mask.tiff
md5:39baefa0717cf6f8a06308b5053d9921
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-07_full_mask.tiff
md5:06605bdbf43774e09aef54224c7455d3
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-08_full_mask.tiff
md5:5617c4263843aaf5eb913b7f2cfec370
738.3 kB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-09_full_mask.tiff
md5:0300616430606fcf265627b458d292a7
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-10_full_mask.tiff
md5:359ca6079adf74be018daa594163bfad
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-11_full_mask.tiff
md5:7734ade8fe4fe088aa54654e47fe6016
4.3 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-12_full_mask.tiff
md5:426cebb8f9a2383092a11e7b15c6e398
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-13_full_mask.tiff
md5:c32bad0e9944f94a570627ce78c3d0ec
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-14_full_mask.tiff
md5:17fd46d5ecff626964afc851e1818b30
2.0 MB Download
processed/20200722_COVID_28_EARLY/tiffs/20200722_COVID_28_EARLY-15_full_mask.tiff
md5:e13f10fc9a6dac5ce88f528a9d08726e
980.3 kB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-01_full_mask.tiff
md5:c0aef1e3dac92d8d8edeb3297b5e6d9f
1.4 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-02_full_mask.tiff
md5:4657d47468d32e5ceba30449457dfca5
1.7 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-03_full_mask.tiff
md5:9d254b64045adbed55e6142c4c3c6e6e
2.9 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-04_full_mask.tiff
md5:a4f6ec158dd4b2896a49f745204fee3a
3.7 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-05_full_mask.tiff
md5:b78d1a93b2f603d33ba248824ed8d751
2.9 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-06_full_mask.tiff
md5:1324f3b42f5e4b3303b1e977005dee3b
4.1 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-07_full_mask.tiff
md5:6287fd3e2d6e347471447c722a6a8566
3.0 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-08_full_mask.tiff
md5:8427168d47a6198dc61ed23425c7f8db
3.8 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-09_full_mask.tiff
md5:87fa304c9e6902d648d8f9a22b0f713b
2.1 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-10_full_mask.tiff
md5:b607592542a5fe79942908335194b093
2.1 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-11_full_mask.tiff
md5:e0c479936dc949cb2bc95a5ce1bfc2b1
3.8 MB Download
processed/20200724_COVID_24_LATE/tiffs/20200724_COVID_24_LATE-12_full_mask.tiff
md5:fba8e2426907b4839dd25e5fedc2e29e
1.3 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-01_full_mask.tiff
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2.0 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-02_full_mask.tiff
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2.9 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-03_full_mask.tiff
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6.7 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-04_full_mask.tiff
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4.3 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-05_full_mask.tiff
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5.8 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-06_full_mask.tiff
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4.8 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-07_full_mask.tiff
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2.6 MB Download
processed/20200728_NL6699/tiffs/20200728_NL6699-08_full_mask.tiff
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1.4 MB Download
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1.8 MB Download
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md5:0617cdffa9b30893fb4fbbf7ee4f7308
5.0 MB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-03_full_mask.tiff
md5:c152842570484a321a24cec66400818d
3.0 MB Download
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md5:6f43104da4433f539e6e9001475af27d
1.3 MB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-05_full_mask.tiff
md5:fec73f8091ebe30c4da3eccb43dd7f61
12.2 MB Download
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md5:9c634655a93b2b4c85cc3eceb9beed7a
2.7 MB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-07_full_mask.tiff
md5:49c04a18b4512375fe5a8aff63521756
900.3 kB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-08_full_mask.tiff
md5:ce560e8219f52bf28a1e934c0546a400
1.8 MB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-09_full_mask.tiff
md5:8d3c9c42feb826bd0f057388ea519708
5.1 MB Download
processed/20200804_NL1933A_RUN2/tiffs/20200804_NL1933A_RUN2-10_full_mask.tiff
md5:76ded19eea9e166af034dc23cd3823b0
4.3 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-01_full_mask.tiff
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3.6 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-02_full_mask.tiff
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1.2 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-03_full_mask.tiff
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7.4 MB Download
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3.2 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-05_full_mask.tiff
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3.1 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-06_full_mask.tiff
md5:a9eab951e905ffc8e9c58872efd9df22
2.0 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-07_full_mask.tiff
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3.7 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-08_full_mask.tiff
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6.3 MB Download
processed/20200806_ARDS_PNE1920/tiffs/20200806_ARDS_PNE1920-09_full_mask.tiff
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2.0 MB Download
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3.1 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-02_full_mask.tiff
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3.4 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-03_full_mask.tiff
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3.3 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-04_full_mask.tiff
md5:029792f87a0c21d980ed27b15f726e42
2.0 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-05_full_mask.tiff
md5:3b17cd812fe6f45f95cc15a0c2dc89ac
2.9 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-06_full_mask.tiff
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2.0 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-07_full_mask.tiff
md5:ea0df663c9813bc4fe0349d32af9ca8c
2.0 MB Download
processed/20200807_ARDS_SEPSIS_19142/tiffs/20200807_ARDS_SEPSIS_19142-08_full_mask.tiff
md5:b3c345a866438e7d8507c407f906ea6d
3.4 MB Download
processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-01_full_mask.tiff
md5:a009fa519336133be9959fd515378694
7.9 MB Download
processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-02_full_mask.tiff
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5.5 MB Download
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md5:e1f615cc01c477dad9be362b901c9652
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processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-04_full_mask.tiff
md5:bb760e2c968e31cc2d28ae9fb92dbf2d
2.9 MB Download
processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-05_full_mask.tiff
md5:6ee8eb81b4ffa905dd5ef0ac524509a0
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processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-06_full_mask.tiff
md5:a10e2f72ddbc8588eb4a9cb9c3b94aa5
2.0 MB Download
processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-07_full_mask.tiff
md5:9c9508978778e420ae74dfef6a6d4d6f
2.8 MB Download
processed/20200810_ARDS_SEPSIS_19135/tiffs/20200810_ARDS_SEPSIS_19135-08_full_mask.tiff
md5:cea02573187eb0f7f1fcaaac5a49cd84
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processed/20200812_ARDS_SEPSIS_1966/tiffs/20200812_ARDS_SEPSIS_1966-01_full_mask.tiff
md5:5a8b64a96ecf866cc24a2346d337abb1
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processed/20200812_ARDS_SEPSIS_1966/tiffs/20200812_ARDS_SEPSIS_1966-02_full_mask.tiff
md5:b9075665c51a7f577c9e1276eb6002f2
6.6 MB Download
processed/20200812_ARDS_SEPSIS_1966/tiffs/20200812_ARDS_SEPSIS_1966-03_full_mask.tiff
md5:85fb3a29501705731d1ec9a52fa959c5
1.6 MB Download
processed/20200812_ARDS_SEPSIS_1966/tiffs/20200812_ARDS_SEPSIS_1966-04_full_mask.tiff
md5:c659e2126a5ee15289d6573e78596914
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processed/20200812_ARDS_SEPSIS_1966/tiffs/20200812_ARDS_SEPSIS_1966-05_full_mask.tiff
md5:3b1e0ef08e78956c419f0cfc1dba7454
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results/covid-imc.h5ad
md5:7fc88292d44045be067a4af162b40292
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