Dataset Open Access
Kylies, Dominik; Zimmermann, Marina; Haas, Fabian; Schwerk, Maria; Kuehl, Malte; Brehler, Michael; Czogalla, Jan; Hernandez, Lola C.; Konczalla, Leonie; Okabayashi, Yusuke; Menzel, Julia; Edenhofer, Ilka; Mezher, Sam; Aypek, Hande; Dumoulin, Bernhard; Wu, Hui; Hofmann, Smilla; Kretz, Oliver; Wanner, Nicola; Tomas, Nicola M.; Krasemann, Susanne; Glatzel, Markus; Kuppe, Christoph; Kramann, Rafael; Banjanin, Bella; Schneider, Rebekka K.; Urbschat, Christopher; Arck, Petra; Gagliani, Nicola; van Zandvoort, Marc; Wiech, Thorsten; Grahammer, Florian; Sáez, Pablo J.; Wong, Milagros N.; Bonn, Stefan; Huber, Tobias B,; Puelles, Victor G.
Expansion microscopy physically enlarges biological specimens to achieve nanoscale resolution using diffraction-limited microscopy systems. However, optimal performance is usually reached using laser-based systems (for example, confocal microscopy), restricting its broad applicability in clinical pathology, as most centres have access only to light-emitting diode (LED)-based widefield systems. As a possible alternative, a computational method for image resolution enhancement, namely, super-resolution radial fluctuations (SRRF), has recently been developed. However, this method has not been explored in pathology specimens to date, because on its own, it does not achieve sufficient resolution for routine clinical use. Here, we report expansion-enhanced super-resolution radial fluctuations (ExSRRF), a simple, robust, scalable and accessible workflow that provides a resolution of up to 25 nm using LED-based widefield microscopy. ExSRRF enables molecular profiling of subcellular structures from archival formalin-fixed paraffin-embedded tissues in complex clinical and experimental specimens, including ischaemic, degenerative, neoplastic, genetic and immune-mediated disorders. Furthermore, as examples of its potential application to experimental and clinical pathology, we show that ExSRRF can be used to identify and quantify classical features of endoplasmic reticulum stress in the murine ischaemic kidney and diagnostic ultrastructural features in human kidney biopsies.
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ext fig 10 3.png
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ext fig 10 4.png
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352.6 kB | Download |
ext fig 10 ExSRRF 0.25 downscale area1.tif
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1.1 MB | Download |
ext fig 10 ExSRRF 0.25 downscale-1.tif
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2.4 MB | Download |
ext fig 10 ExSRRF 1.0 size area1.tif
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1.1 MB | Download |
ext fig 10 IgAN018 G1 S010 ExSRRF raw.tif
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37.8 MB | Download |
ext fig 10 ridges_and_roi_IgAN018 G1 S010 ExSRRF ridge and area.png
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35.0 kB | Download |
ext fig 1a nanoruler.tif
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ext fig 1a plot of selection 1.1.1 r9.tif
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ext fig 1b nanoruler distances.xlsx
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ext fig 1c post.tif
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ext fig 1c pre.tif
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ext fig 1d expansion measurements in tissues.xlsx
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ext fig 2a.tif
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ext fig 3a,b,c.pptx
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28.5 MB | Download |
ext fig 3d,e.tiff
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ext fig 4 ExM region 1 single upscale crop.tif
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ext fig 4 ExM region 2 single upscale crop.tif
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ext fig 4 ExM region 3 single upscale crop.tif
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ext fig 4 ExM scout.tif
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4.2 MB | Download |
ext fig 4 ExSRRF region 1 crop.tif
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ext fig 4 ExSRRF region 2 crop.tif
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ext fig 4 ExSRRF region 3 crop.tif
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ext fig 4 ExSRRF scout.tif
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ext fig 4 SRRF region 1 upscale crop.tif
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ext fig 4 SRRF region 2 upscale crop.tif
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ext fig 4 SRRF region 3 upscale crop.tif
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ext fig 4 SRRF scout.tif
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53.7 MB | Download |
ext fig 4 WF region 1 upscale crop.tif
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ext fig 4 WF region 2 upscale crop.tif
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ext fig 4 WF region 3 upscale crop.tif
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117.1 kB | Download |
ext fig 4 WF scout.tif
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416.8 kB | Download |
ext fig 5a after correction c1=post exp raw c2=ExSRRF c3=error map c4= convolved with RSF.tif
md5:b6c8c4d581d504edef2f53f3256bd4ce |
21.7 MB | Download |
ext fig 5a before correction c1=post exp raw c2=ExSRRF c3=error map c4= convolved with RSF.tif
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21.3 MB | Download |
ext fig 5b.xlsx
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ext fig 6 damage score and apoptosis.xlsx
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ext fig 7a high magnification.tif
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ext fig 7a overview.tif
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ext fig 7b.tif
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ext fig 7c high magnification.tif
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ext fig 7c overview.tif
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ext fig 7d high magnification.tif
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6.3 MB | Download |
ext fig 7d overview.tif
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136.1 MB | Download |
ext fig 7e high magnification.tif
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6.9 MB | Download |
ext fig 7e overview.tif
md5:9760495fa4cd91c7a2a9a0985ed5de06 |
469.8 MB | Download |
ext fig 8a human kidney SD c1 ExM c2 ExM ridges c3 ExSRRF c4 ExSRRF ridges.tif
md5:977d01b745e9a20dac4f75657dd2d36a |
7.8 MB | Download |
ext fig 8a human kidney SD c1 STED c2 STED ridges.tif
md5:25933898ac4cd061a33efc799f1b6e0d |
1.6 MB | Download |
ext fig 8a murine kidney ER c1 ExM c2 ExM ridges c3 ExSRRF c4 ExSRRF ridges.tif
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522.5 kB | Download |
ext fig 8b ER_stress_exsrrf_ex_evaluation_SSIM.xlsx
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ext fig 8b Nephrin_exsrrf_ex_evaluation_SSIM.xlsx
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ext fig 8b STED_exsrrf_ex_evaluation_SSIM.xlsx
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52.4 kB | Download |
ext fig 9 IgA_009_d-1.tif
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ext fig 9 IgA_009_d-2.tif
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ext fig 9 MCD_021_d-1.tif
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1.3 MB | Download |
ext fig 9 MCD_021_d-2.tif
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fig 1c 1.tif
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fig 1c 2.tif
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fig 1c 3.tif
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fig 1c 4.tif
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6.8 MB | Download |
fig 1d 1.tif
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172.7 MB | Download |
fig 1d 2.tif
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fig 1d 3.tif
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fig 1d 4.tif
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fig 1d 5.tif
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268.4 MB | Download |
fig 1e 1.tif
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fig 1e 2 VMT.tif
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fig 1e 3 amyloid.tif
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fig 1e 4.tif
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fig 1e 5 VMT.tif
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64.0 MB | Download |
fig 1e 6 amyloid.tif
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64.0 MB | Download |
fig 1g colitis data.pzfx
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9.0 kB | Download |
fig 1g.xlsx
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9.4 kB | Download |
fig 1h 1 ctrl.tif
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231.8 MB | Download |
fig 1h 2 ctrl.tif
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8.2 MB | Download |
fig 1h 3 ctrl.tif
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8.2 MB | Download |
fig 1h 4 colitis.tif
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231.8 MB | Download |
fig 1h 5 colitis.tif
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8.2 MB | Download |
fig 1h 6 colitis.tif
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8.2 MB | Download |
fig 1h proximity colitis.xlsx
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10.0 kB | Download |
fig 1h proximity ctrl.xlsx
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9.9 kB | Download |
fig 1j ex1 altered ExSRRF.tif
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6.2 MB | Download |
fig 1j ex1 altered WF.tif
md5:bdd7de81bcdd9ce4774996f0eae0e3a4 |
1.0 MB | Download |
fig 1j ex1 normal ExSRRF.tif
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6.2 MB | Download |
fig 1j ex1 normal WF.tif
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1.3 MB | Download |
fig 1j ex2 altered ExSRRF.tif
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6.2 MB | Download |
fig 1j ex2 altered WF.tif
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1.0 MB | Download |
fig 1j ex2 normal ExSRRF.tif
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6.2 MB | Download |
fig 1j ex2 normal WF.tif
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1.3 MB | Download |
fig 2b 120nm post.tif
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207.0 kB | Download |
fig 2b 120nm pre.tif
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82.2 kB | Download |
fig 2b 25nm post.tif
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207.0 kB | Download |
fig 2b 25nm pre.tif
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82.2 kB | Download |
fig 2b 30nm post.tif
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207.0 kB | Download |
fig 2b 30nm pre.tif
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fig 2b 40nm post.tif
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207.0 kB | Download |
fig 2b 40nm pre.tif
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fig 2b 80nm post.tif
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207.0 kB | Download |
fig 2b 80nm pre.tif
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82.2 kB | Download |
fig 2c not resolved.tif
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77.0 kB | Download |
fig 2c quantification data.xlsx
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55.7 kB | Download |
fig 2c resolved.tif
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293.4 kB | Download |
fig 2d ExSRRF 1.tif
md5:b339c12b1ff8d2673bdfbe7b50cc0eb9 |
87.8 MB | Download |
fig 2d ExSRRF 2.tif
md5:10a00ae3d3d48a77a30e9d21ade6aa73 |
104.9 MB | Download |
fig 2d ExSRRF 3.tif
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11.5 MB | Download |
fig 2d STED 1.tif
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3.6 MB | Download |
fig 2d STED 2.tif
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686.4 kB | Download |
fig 2d STED 3.tif
md5:ff1dd783a0f3683122fc4b1bd43ca760 |
71.9 kB | Download |
fig 2e ExSRRF.tif
md5:1999c8618a4b65a8beba1c28a2ee4d52 |
1.0 MB | Download |
fig 2e STED.tif
md5:e582aad3ea3b7a224aab115dde24d0f5 |
1.0 MB | Download |
fig 2e tissue overview.tif
md5:ee03ab378ae3f00cb31b39e566dd8165 |
391.1 MB | Download |
fig 2f area 1 ExSRRF STED.tif
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2.0 MB | Download |
fig 2f area 2 ExSRRF STED.tif
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2.1 MB | Download |
fig 2f area 3 ExSRRF STED.tif
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2.0 MB | Download |
fig 2h,j nephrin_Overall_MSSIM_MSE.xlsx
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14.3 kB | Download |
fig 2i example 1 after.tif
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361.8 kB | Download |
fig 2i example 1 before.tif
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361.8 kB | Download |
fig 2i example 1 raw.tif
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fig 2i example 2 after.tif
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fig 2i example 2 before.tif
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361.8 kB | Download |
fig 2i example 2 raw.tif
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2.3 kB | Download |
fig 2k ctrl EM.tif
md5:d527c4e77e7c9183fec5d2776e7b19ab |
4.3 MB | Download |
fig 2k ctrl ExSRRF high magnification.tif
md5:c4d2f76314d6795e5a2527db6a5fb3f6 |
86.5 kB | Download |
fig 2k ctrl ExSRRF.tif
md5:7e170e0dc62ddf0c5126e49d20be53b5 |
34.3 MB | Download |
fig 2k ischemia EM.tif
md5:ee58dd93dd23b38a251835afd867f80e |
4.3 MB | Download |
fig 2k ischemia ExSRRF.tif
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17.1 MB | Download |
fig 2l 1.tif
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23.8 MB | Download |
fig 2l 2.tif
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11.9 MB | Download |
fig 2l density.xlsx
md5:61c23704aa7edeff36e4e023a6d005ab |
5.4 kB | Download |
fig 2l ridges 1.tif
md5:898c4155112f5fdd029c74e345d19cd3 |
3.0 MB | Download |
fig 2l ridges 2.tif
md5:38291f6fed0a08410ff2dffa9764503c |
3.0 MB | Download |
fig 2l spacing 1.tif
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3.0 MB | Download |
fig 2l spacing 2.tif
md5:ed0194e9352bc586d1b8a80dbd1b3467 |
3.0 MB | Download |
fig 2l spacing.xlsx
md5:b2023f96ab5b5d5145ebd952d4e4828f |
6.2 kB | Download |
fig 3b full tissue scout.tif
md5:b8ed42017ec12bb7596197b8ed2b900f |
682.7 MB | Download |
fig 3b normal 1.tif
md5:bd026067e7b78b399a7fd9e792f7cfce |
25.2 MB | Download |
fig 3b normal baseline 2.tif
md5:c46e633d5197c56bae8a5edffe217673 |
947.3 kB | Download |
fig 3b normal baseline 3.tif
md5:38ecc1de5e35323b3a5195be01dabde9 |
87.0 kB | Download |
fig 3b normal exsrrf 4.tif
md5:e4605441bf2fcb799d356839cd73eb7b |
12.0 MB | Download |
fig 3b normal exsrrf.tif
md5:355a2036c554046a8557641d34291646 |
113.2 MB | Download |
fig 3b patho baseline 5.tif
md5:35e02c8e3796d979ae717b521dc419da |
8.2 kB | Download |
fig 3b patho baseline.tif
md5:c97bc557dcd730997cd3fa1257a909c9 |
387.2 kB | Download |
fig 3b patho exsrrf 6.tif
md5:db7a443e4b04478939540f13d8050122 |
12.0 MB | Download |
fig 3b patho exsrrf.tif
md5:2c2197f1f530030bcf497f8fd78c0840 |
113.2 MB | Download |
fig 3c IgAN baseline region 7.tif
md5:67fd0c61db17dd147e2b4389b2a69eec |
18.7 kB | Download |
fig 3c IgAN baseline.tif
md5:9ee67c885c16bbc2e6b671048bccf529 |
246.3 kB | Download |
fig 3c IgAN exsrrf region 9.tif
md5:ae57b7113e711f77889d9a77e2152a94 |
23.0 MB | Download |
fig 3c IgAN exsrrf.tif
md5:768bd5d8af94fdaf610c7a4a0bd9ebb0 |
75.5 MB | Download |
fig 3c MCD baseline region 8.tif
md5:4b587a923dd24d00a77d1b6fd6ecfc1d |
10.5 kB | Download |
fig 3c MCD baseline.tif
md5:4027a2e4eced8f8e7de6917c7a97cc5f |
320.2 kB | Download |
fig 3c MCD exsrrf region 10.tif
md5:54f0397909953c05609cb46870ddf7ed |
17.3 MB | Download |
fig 3c MCD exsrrf.tif
md5:78d8a26aed8619e124df4bccd5f98d11 |
75.5 MB | Download |
fig 3d IgAN.png
md5:c80c3bf4ac7072722f7cf40f2ca8f810 |
100.0 kB | Download |
fig 3d MCD.png
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65.3 kB | Download |
fig 3e,h density analysis.xlsx
md5:63c1bde67145f677d141ca20003d3bef |
44.8 kB | Download |
fig 3f IgAN.png
md5:53c432cbea4b486e6f36cd17ec4b4ae4 |
442.0 kB | Download |
fig 3f MCD.png
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357.9 kB | Download |
fig 3g,i spacing analysis.xlsx
md5:6ce5a4595bac6f4b5001e207ffe77362 |
12.7 kB | Download |
fig 3j IgAN.tif
md5:b68ebe4e5f2ca25ee1abfd72245a3d17 |
10.3 MB | Download |
fig 3j MCD.tif
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10.3 MB | Download |
fig 3k,l,m FP width.xlsx
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12.5 kB | Download |
fig 3k,l,m SD width.xlsx
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12.3 kB | Download |
fig_1b_1.tif
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1.0 GB | Download |
fig_1b_2.tif
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5.8 MB | Download |
fig_1b_3.tif
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1.8 MB | Download |
fig_1b_4.tif
md5:1c2aba1ae03245c34792b6f7abb5abdd |
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