Fischer TM, Stöhr-Lissen M, Schmid-Schönbein H. 1978. The red cell as a fluid droplet: tank tread-like motion of the human erythrocyte membrane in shear flow. Science **202**:894-896. DOI: https://doi.org/10.1126/science.715448, PMID: 715448

Frank RS. 1990. Time-dependent alterations in the deformability of human neutrophils in response to chemotactic activation. *Blood* **76**:2606-2612. DOI: https://doi.org/10.1182/blood.V76.12.2606.2606, PMID: 2265253

Fregin B. Czerwinski F, Biedenweg D, Girardo S, Gross S, Aurich K, Otto O. 2019. High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry. *Nature Communications* **10**:415. DOI: https://doi.org/10.1038/s41467-019-08370-3, PMID: 30679420

Gerum R. 2022. Shear flow deformation cytometer. swh:1:rev:2d35a697243c432cddd52e10d2e3c5121f922adf. Software Heritage. https://archive.softwareheritage.org/swh:1:dir:67564c98bd49cc7dac9bcb61117e8ce813d480df;origin=https://github.com/fabrylab/shear_flow_deformation_cytometer;visit=swh:1:snp:1076b5f65c6e2d71c86d2705df6a821d2ab125db;anchor=swh:1:rev:2d35a697243c432cddd52e10d2e3c5121f922adf

Girardo S, Träber N, Wagner K, Cojoc G, Herold C, Goswami R, Schlüßler R, Abuhattum S, Taubenberger A, Reichel F, Mokbel D, Herbig M, Schürmann M, Müller P, Heida T, Jacobi A, Ulbricht E, Thiele J, Werner C, Guck J. 2018. Standardized microgel beads as elastic cell mechanical probes. *Journal of Materials Chemistry. B* **6**:6245-6261. DOI: https://doi.org/10.1039/c8tb01421c, PMID: 32254615

Gossett DR, Tse HTK, Lee SA, Ying Y, Lindgren AG, Yang OO, Rao J, Clark AT, Di Carlo D. 2012. Hydrodynamic stretching of single cells for large population mechanical phenotyping. *PNAS* **109**:7630-7635. DOI: https://doi.org/10.1073/pnas.1200107109, PMID: 22547795

Gregor M, Osmanagic-Myers S, Burgstaller G, Wolfram M, Fischer I, Walko G, Resch GP, Jörgl A, Herrmann H, Wiche G. 2014. Mechanosensing through focal adhesion-anchored intermediate filaments. *FASEB Journal* **28**:715-729. DOI: https://doi.org/10.1096/fj.13-231829, PMID: 24347609

Hecht FM, Rheinlaender J, Schierbaum N, Goldmann WH, Fabry B, Schäffer TE. 2015. Imaging viscoelastic properties of live cells by afm: power-law rheology on the nanoscale. *Soft Matter* **11**:4584-4591. DOI: https://doi.org/10.1039/c4sm02718c, PMID: 25891371

Herrmann H, Cabet E, Chevalier NR, Moosmann J, Schultheis D, Haas J, Schowalter M, Berwanger C, Weyerer V, Agaimy A, Meder B, Müller OJ, Katus HA, Schlötzer-Schrehardt U, Vicart P, Ferreiro A, Dittrich S, Clemen CS, Lilienbaum A, Schröder R. 2020. Dual functional states of r406w-desmin assembly complexes cause cardiomyopathy with severe intercalated disc derangement in humans and in knock-in mice. *Circulation* **142**:2155-2171. DOI: https://doi.org/10.1161/CIRCULATIONAHA.120.050218, PMID: 33023321

Hutter JL, Bechhoefer J. 1993. Calibration of atomic-force microscope tips. *The Review of Scientific Instruments* **64**:1868-1873. DOI: https://doi.org/10.1063/1.1143970

Kalcioğlu ZI, Mahmoodian R, Hu YH, Suo ZG, Van Vliet KJ. 2012. From macro- to microscale poroelastic characterization of polymeric hydrogels via indentation. *Soft Matter* **8**:3393. DOI: https://doi.org/10.1039/c2sm06825g

Lange JR, Steinwachs J, Kolb T, Lautscham LA, Harder I, Whyte G, Fabry B. 2015. Microconstriction arrays for high-throughput quantitative measurements of cell mechanical properties. *Biophysical Journal* **109**:26-34. DOI: https://doi.org/10.1016/j.bpj.2015.05.029, PMID: 26153699

Lange JR, Metzner C, Richter S, Schneider W, Spermann M, Kolb T, Whyte G, Fabry B. 2017. Unbiased high-precision cell mechanical measurements with microconstrictions. *Biophysical Journal* **112**:1472-1480. DOI: https://doi.org/10.1016/j.bpj.2017.02.018, PMID: 28402889

Mietke A, Otto O, Girardo S, Rosendahl P, Taubenberger A, Golfier S, Ulbricht E, Aland S, Guck J, Fischer-Friedrich E. 2015. Extracting cell stiffness from real-time deformability cytometry: theory and experiment. *Biophysical Journal* **109**:2023-2036. DOI: https://doi.org/10.1016/j.bpj.2015.09.006, PMID: 26588562

Müller SJ, Mirzahossein E, Iftekhar EN, Bächer C, Schrüfer S, Schubert DW, Fabry B, Gekle S, Tian F-B. 2007. Flow and hydrodynamic shear stress inside a printing needle during biofabrication. *PLOS ONE* **15**:e0236371. DOI: https://doi.org/10.1371/journal.pone.0236371

Otto O, Rosendahl P, Mietke A, Golfier S, Herold C, Klaue D, Girardo S, Pagliara S, Ekpenyong A, Jacobi A, Wobus M, Töpfner N, Keyser UF, Mansfeld J, Fischer-Friedrich E, Guck J. 2015. Real-time deformability cytometry: on-the-fly cell mechanical phenotyping. *Nature Methods* **12**:199-202. DOI: https://doi.org/10.1038/nmeth.3281, PMID: 25643151

Patteson AE, Carroll RJ, Iwamoto DV, Janmey PA. 2020. The vimentin cytoskeleton: when polymer physics meets cell biology. *Physical Biology* **18**:011001. DOI: https://doi.org/10.1088/1478-3975/abbcc2, PMID: 32992303

Ronneberger O, Fischer P, Brox T. 2015. U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention. 234-241. DOI: https://doi.org/10.1007/978-3-319-24574-4

Roscoe R. 1967. On the rheology of a suspension of viscoelastic spheres in a viscous liquid. *Journal of Fluid Mechanics* **28**:273. DOI: https://doi.org/10.1017/S002211206700206X

Rowat AC, Jaalouk DE, Zwerger M, Ung WL, Eydelnant IA, Olins DE, Olins AL, Herrmann H, Weitz DA, Lammerding J. 2012. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. *Journal of Biological Chemistry* **288**:8610-8618. DOI: https://doi.org/10.1074/jbc.M112.441535, PMID: 23355469

Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, Kashiwagi S, Fukami K, Miyata T, Miyoshi H, Imamura T, Ogawa M, Masai H, Miyawaki A. 2008. Visualizing spatiotemporal dynamics of
Fischer TM, Stöhr-Lissen M, Schmid-Schönbein H. 1978. The red cell as a fluid droplet: tank tread-like motion of the human erythrocyte membrane in shear flow. Science **202**:894–896. DOI: https://doi.org/10.1126/science.715448, PMID: 715448

Frank RS. 1990. Time-dependent alterations in the deformability of human neutrophils in response to chemotactic activation. *Blood* **76**:2606–2612. DOI: https://doi.org/10.1182/blood.V76.12.2606.2606, PMID: 2265253

Fregin B. Czerwinski F, Biedenweg D, Girardo S, Gross S, Aurich K, Otto O. 2019. High-throughput single-cell rheology in complex samples by dynamic real-time deformability cytometry. *Nature Communications* **10**:415. DOI: https://doi.org/10.1038/s41467-019-08370-3, PMID: 30679420

Gerum R. 2022. Shear flow deformation cytometer. swh:1:rev:2d35a697243c432cddd52e10d2e3c5121f922adf. Software Heritage. https://archive.softwareheritage.org/swh:1:dir:67564c98bd49cc7dac9bcb61117e8ce813d480df;origin=https://github.com/fabrylab/shear_flow_deformation_cytometer;visit=swh:1:snp:1076b5f65c6e2d71c86d2705df6a821d2ab125db;anchor=swh:1:rev:2d35a697243c432cddd52e10d2e3c5121f922adf

Girardo S, Träber N, Wagner K, Cojoc G, Herold C, Goswami R, Schlüßler R, Abuhattum S, Taubenberger A, Reichel F, Mokbel D, Herbig M, Schürmann M, Müller P, Heida T, Jacobi A, Ulbricht E, Thiele J, Werner C, Guck J. 2018. Standardized microgel beads as elastic cell mechanical probes. *Journal of Materials Chemistry. B* **6**:6245–6261. DOI: https://doi.org/10.1039/c8tb01421c, PMID: 32254615

Gossett DR, Tse HTK, Lee SA, Ying Y, Lindgren AG, Yang OO, Rao J, Clark AT, Di Carlo D. 2012. Hydrodynamic stretching of single cells for large population mechanical phenotyping. *PNAS* **109**:7630–7635. DOI: https://doi.org/10.1073/pnas.1200107109, PMID: 22547795

Gregor M, Osmanagic-Myers S, Burgstaller G, Wolfram M, Fischer I, Walko G, Resch GP, Jörgl A, Herrmann H, Wiche G. 2014. Mechanosensing through focal adhesion-anchored intermediate filaments. *FASEB Journal* **28**:715–729. DOI: https://doi.org/10.1096/fj.13-231829, PMID: 24347609

Hecht FM, Rheinlaender J, Schierbaum N, Goldmann WH, Fabry B, Schäffer TE. 2015. Imaging viscoelastic properties of live cells by afm: power-law rheology on the nanoscale. *Soft Matter* **11**:4584–4591. DOI: https://doi.org/10.1039/c4sm02718c, PMID: 25891371

Herrmann H, Cabet E, Chevalier NR, Moosmann J, Schultheis D, Haas J, Schowalter M, Berwanger C, Weyerer V, Agaimy A, Meder B, Müller OJ, Katus HA, Schlötzer-Schrehardt U, Vicart P, Ferreiro A, Dittrich S, Clemen CS, Lilienbaum A, Schröder R. 2020. Dual functional states of r406w-desmin assembly complexes cause cardiomyopathy with severe intercalated disc derangement in humans and in knock-in mice. *Circulation* **142**:2155–2171. DOI: https://doi.org/10.1161/CIRCULATIONAHA.120.050218, PMID: 33023321

Hutter JL, Bechhoefer J. 1993. Calibration of atomic-force microscope tips. *The Review of Scientific Instruments* **64**:1868–1873. DOI: https://doi.org/10.1063/1.1143970

Kalcioğlu ZI, Mahmoodian R, Hu YH, Suo ZG, Van Vliet KJ. 2012. From macro- to microscale poroelastic characterization of polymeric hydrogels via indentation. *Soft Matter* **8**:3393. DOI: https://doi.org/10.1039/c2sm06825g

Lange JR, Steinwachs J, Kolb T, Lautscham LA, Harder I, Whyte G, Fabry B. 2015. Microconstriction arrays for high-throughput quantitative measurements of cell mechanical properties. *Biophysical Journal* **109**:26–34. DOI: https://doi.org/10.1016/j.bpj.2015.05.029, PMID: 26153699

Lange JR, Metzner C, Richter S, Schneider W, Spermann M, Kolb T, Whyte G, Fabry B. 2017. Unbiased high-precision cell mechanical measurements with microconstrictions. *Biophysical Journal* **112**:1472–1480. DOI: https://doi.org/10.1016/j.bpj.2017.02.018, PMID: 28402889

Mietke A, Otto O, Girardo S, Rosendahl P, Taubenberger A, Golfier S, Ulbricht E, Aland S, Guck J, Fischer-Friedrich E. 2015. Extracting cell stiffness from real-time deformability cytometry: theory and experiment. *Biophysical Journal* **109**:2023–2036. DOI: https://doi.org/10.1016/j.bpj.2015.09.006, PMID: 26588562

Müller SJ, Mirzahossein E, Iftekhar EN, Bächer C, Schrüfer S, Schubert DW, Fabry B, Gekle S, Tian F-B. 2007. Flow and hydrodynamic shear stress inside a printing needle during biofabrication. *PLOS ONE* **15**:e0236371. DOI: https://doi.org/10.1371/journal.pone.0236371

Otto O, Rosendahl P, Mietke A, Golfier S, Herold C, Klaue D, Girardo S, Pagliara S, Ekpenyong A, Jacobi A, Wobus M, Töpfner N, Keyser UF, Mansfeld J, Fischer-Friedrich E, Guck J. 2015. Real-time deformability cytometry: on-the-fly cell mechanical phenotyping. *Nature Methods* **12**:199–202. DOI: https://doi.org/10.1038/nmeth.3281, PMID: 25643151

Patteson AE, Carroll RJ, Iwamoto DV, Janmey PA. 2020. The vimentin cytoskeleton: when polymer physics meets cell biology. *Physical Biology* **18**:011001. DOI: https://doi.org/10.1088/1478-3975/abbcc2, PMID: 32992303

Ronneberger O, Fischer P, Brox T. 2015. U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention. 234–241. DOI: https://doi.org/10.1007/978-3-319-24574-4

Roscoe R. 1967. On the rheology of a suspension of viscoelastic spheres in a viscous liquid. *Journal of Fluid Mechanics* **28**:273. DOI: https://doi.org/10.1017/S002211206700206X

Rowat AC, Jaalouk DE, Zwerger M, Ung WL, Eydelnant IA, Olins DE, Olins AL, Herrmann H, Weitz DA, Lammerding J. 2012. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. *Journal of Biological Chemistry* **288**:8610–8618. DOI: https://doi.org/10.1074/jbc.M112.441535, PMID: 23355469

Sakaue-Sawano A, Kurokawa H, Morimura T, Hanyu A, Hama H, Osawa H, Kashiwagi S, Fukami K, Miyata T, Miyoshi H, Imamura T, Ogawa M, Masai H, Miyawaki A. 2008. Visualizing spatiotemporal dynamics of
multicellular cell-cycle progression. **Cell** **132**:487-498. DOI: https://doi.org/10.1016/j.cell.2007.12.033, PMID: 18267078

Schmid-Schöenbein H, Wells R. 1969. Fluid drop-like transition of erythrocytes under shear. *Science* **165**:288-291. DOI: https://doi.org/10.1126/science.165.3890.288, PMID: 5787985

Silverman BW. 1965. Density Estimation for Statistics and Data Analysis. Routledge. DOI: https://doi.org/10.1201/9781315140919

Smith BA, Tollozko B, Martin JG, Grütter P. 2005. Probing the viscoelastic behavior of cultured airway smooth muscle cells with atomic force microscopy: stiffening induced by contractile agonist. *Biophysical Journal* **88**:2994-3007. DOI: https://doi.org/10.1529/biophysj.104.046649, PMID: 15665124

Snijkers F, D'Avino G, Maffettone PL, Greco F, Hulsen MA, Vermant J. 2011. Effect of viscoelasticity on the rotation of a sphere in shear flow. *Journal of Non-Newtonian Fluid Mechanics* **166**:363-372. DOI: https://doi.org/10.1016/j.jnnfm.2011.01.004

Sollich P. 1998. Rheological constitutive equation for a model of soft glassy materials. *Physical Review E* **58**:738-759. DOI: https://doi.org/10.1103/PhysRevE.58.738

Stewart MP, Hodel AW, Spielhofer A, Cattin CJ, Müller DJ, Helenius J. 2013. Wedged afm-cantilevers for parallel plate cell mechanics. *Methods* **60**:186-194. DOI: https://doi.org/10.1016/j.ymeth.2013.02.015, PMID: 23473778

Sumbul F, Hassanpour N, Rodriguez-Ramos J, Rico F. 2020. One-step calibration of afm in liquid. *Frontiers in Physics* **8**:301. DOI: https://doi.org/10.3389/fphy.2020.00301

Svitkina TM, Verkhovsky AB, Borisy GG. 1996. Plectin sidearms mediate interaction of intermediate filaments with microtubules and other components of the cytoskeleton. *The Journal of Cell Biology* **135**:991-1007. DOI: https://doi.org/10.1083/jcb.135.4.991, PMID: 8922382

Todaro GJ, Green H. 1963. Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines. *The Journal of Cell Biology* **17**:299-313. DOI: https://doi.org/10.1083/jcb.17.2.299, PMID: 13985244

Urbanska M, Muñoz HE, Shaw Bagnall J, Otto O, Manalis SR, Di Carlo D, Guck J. 2020. A comparison of microfluidic methods for high-throughput cell deformability measurements. *Nature Methods* **17**:587-593. DOI: https://doi.org/10.1038/s41592-020-0818-8, PMID: 32341544

van der Walt S, Schönberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, Gouillart E, Yu T, scikit-image contributors. 2014. Scikit-image: image processing in python. *PeerJ* **2**:e453. DOI: https://doi.org/10.7717/peerj.453, PMID: 25024921

Van Rossum G, Drake FL. 2009. Python 3 Reference Manual. Scotts Valley, CA: CreateSpace.

Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, et al. 2020. SciPy 1.0: fundamental algorithms for scientific computing in python. *Nature Methods* **17**:261-272. DOI: https://doi.org/10.1038/s41592-019-0686-2, PMID: 32015543

Wu H, Shen Y, Sivagurunathan S, Weber MS, Adam SA, Shin JH, Fredberg JJ, Medalia O, Goldman R, Weitz DA. 2022. Vimentin intermediate filaments and filamentous actin form unexpected interpenetrating networks that redefine the cell cortex. *PNAS* **119**:e2115217119. DOI: https://doi.org/10.1073/pnas.2115217119, PMID: 35235449

Zach C, Pock T, Bischof H. 2007. A duality based approach for realtime tv-l1 optical flow. Hamprecht FA, Schnörr C, Jähne B (Eds). *Pattern Recognition*. Berlin Heidelberg: Springer. p. 214-233. DOI: https://doi.org/10.1007/978-3-540-74936-3

Zhelev DV, Needham D, Hochmuth RM. 1994. Role of the membrane cortex in neutrophil deformation in small pipets. *Biophysical Journal* **67**:696-705. DOI: https://doi.org/10.1016/S0006-3495(94)80529-6, PMID: 7948682
multicellular cell-cycle progression. **Cell** **132**:487-498. DOI: https://doi.org/10.1016/j.cell.2007.12.033, PMID: 18267078

Schmid-Schöenbein H, Wells R. 1969. Fluid drop-like transition of erythrocytes under shear. *Science* **165**:288-291. DOI: https://doi.org/10.1126/science.165.3890.288, PMID: 5787985

Silverman BW. 1965. Density Estimation for Statistics and Data Analysis. Routledge. DOI: https://doi.org/10.1201/9781315140919

Smith BA, Tollozko B, Martin JG, Grütter P. 2005. Probing the viscoelastic behavior of cultured airway smooth muscle cells with atomic force microscopy: stiffening induced by contractile agonist. *Biophysical Journal* **88**:2994-3007. DOI: https://doi.org/10.1529/biophysj.104.046649, PMID: 15665124

Snijkers F, D'Avino G, Maffettone PL, Greco F, Hulsen MA, Vermant J. 2011. Effect of viscoelasticity on the rotation of a sphere in shear flow. *Journal of Non-Newtonian Fluid Mechanics* **166**:363-372. DOI: https://doi.org/10.1016/j.jnnfm.2011.01.004

Sollich P. 1998. Rheological constitutive equation for a model of soft glassy materials. *Physical Review E* **58**:738-759. DOI: https://doi.org/10.1103/PhysRevE.58.738

Stewart MP, Hodel AW, Spielhofer A, Cattin CJ, Müller DJ, Helenius J. 2013. Wedged afm-cantilevers for parallel plate cell mechanics. *Methods* **60**:186-194. DOI: https://doi.org/10.1016/j.ymeth.2013.02.015, PMID: 23473778

Sumbul F, Hassanpour N, Rodriguez-Ramos J, Rico F. 2020. One-step calibration of afm in liquid. *Frontiers in Physics* **8**:301. DOI: https://doi.org/10.3389/fphy.2020.00301

Svitkina TM, Verkhovsky AB, Borisy GG. 1996. Plectin sidearms mediate interaction of intermediate filaments with microtubules and other components of the cytoskeleton. *The Journal of Cell Biology* **135**:991-1007. DOI: https://doi.org/10.1083/jcb.135.4.991, PMID: 8922382

Todaro GJ, Green H. 1963. Quantitative studies of the growth of mouse embryo cells in culture and their development into established lines. *The Journal of Cell Biology* **17**:299-313. DOI: https://doi.org/10.1083/jcb.17.2.299, PMID: 13985244

Urbanska M, Muñoz HE, Shaw Bagnall J, Otto O, Manalis SR, Di Carlo D, Guck J. 2020. A comparison of microfluidic methods for high-throughput cell deformability measurements. *Nature Methods* **17**:587-593. DOI: https://doi.org/10.1038/s41592-020-0818-8, PMID: 32341544

van der Walt S, Schönberger JL, Nunez-Iglesias J, Boulogne F, Warner JD, Yager N, Gouillart E, Yu T, scikit-image contributors. 2014. Scikit-image: image processing in python. *PeerJ* **2**:e453. DOI: https://doi.org/10.7717/peerj.453, PMID: 25024921

Van Rossum G, Drake FL. 2009. Python 3 Reference Manual. Scotts Valley, CA: CreateSpace.

Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, et al. 2020. SciPy 1.0: fundamental algorithms for scientific computing in python. *Nature Methods* **17**:261-272. DOI: https://doi.org/10.1038/s41592-019-0686-2, PMID: 32015543

Wu H, Shen Y, Sivagurunathan S, Weber MS, Adam SA, Shin JH, Fredberg JJ, Medalia O, Goldman R, Weitz DA. 2022. Vimentin intermediate filaments and filamentous actin form unexpected interpenetrating networks that redefine the cell cortex. *PNAS* **119**:e2115217119. DOI: https://doi.org/10.1073/pnas.2115217119, PMID: 35235449

Zach C, Pock T, Bischof H. 2007. A duality based approach for realtime tv-l1 optical flow. Hamprecht FA, Schnörr C, Jähne B (Eds). *Pattern Recognition*. Berlin Heidelberg: Springer. p. 214-233. DOI: https://doi.org/10.1007/978-3-540-74936-3

Zhelev DV, Needham D, Hochmuth RM. 1994. Role of the membrane cortex in neutrophil deformation in small pipets. *Biophysical Journal* **67**:696-705. DOI: https://doi.org/10.1016/S0006-3495(94)80529-6, PMID: 7948682