DOI: 10.5061/dryad.t76hdr88t
title: An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization

description: The mesoscope has emerged as a powerful imaging tool in biomedical
 research, yet its high cost and low resolution have limited its broader
 application. Here, we introduce the Omni-Mesoscope, a
 high-spatial-temporal and multimodal mesoscopic imaging platform built
 from cost-efficient off-the-shelf components. This system uniquely merges
 the capabilities of label-free quantitative phase microscopy to capture
 live-cell morpho-dynamics across thousands of cells with highly
 multiplexed fluorescence imaging for comprehensive molecular
 characterization. This Omni-Mesoscope offers a mesoscale field of view of
 approximately 5 mm² with a high spatial resolution down to 700 nm,
 enabling the capture of detailed sub-cellular features. We demonstrate its
 capability in delineating molecular characteristics underlying rare
 morpho-dynamic cellular phenomena, including cancer cell responses to
 chemotherapy and the emergence of polyploidy in drug-resistant cells. We
 also integrate expansion technique to enhance 3D volumetric
 super-resolution imaging of thicker tissues, opening new avenues for
 biological exploration at unprecedented scales and resolutions.
description: # An Omni-Mesoscope for multiscale high-throughput quantitative phase
 imaging of cellular dynamics and high-content molecular characterization
 [https://doi.org/10.5061/dryad.t76hdr88t](https://doi.org/10.5061/dryad.t76hdr88t) ## Description of the data and file structure #### File: Omni\_Mesoscope\_data.zip **Description:** Image data used in "An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization" **Folder: "Multiplex Fluorescent Images"** This folder contains the stitched fluorescence images of multiple biomarkers, as used in Figure 6 of the main text. "SW480_5Fu_3d_Cy1_H3K27me3_Ex650_Em676_Reg.tiff": H3K27me3 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy1_LMNAC_Ex530_Em572_Reg.tiff": LMNAC channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy2_CENPA_Ex650_Em676_Reg.tiff": CENPA channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy2_H3_Ex405_Em438_Reg.tiff": H3 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy2_Ki67_Ex470_Em510_Reg.tiff": Ki67 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy2_MCM7_Ex589_Em615_Reg.tiff": MCM7 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy3_H2Ax_Ex589_Em615_Reg.tiff": H2Ax channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy3_H3K9me3_Ex650_Em676_Reg.tiff": H3K9me3 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy3_P53_Ex470_Em510_Reg.tiff": P53 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy3_Vmt_Ex530_Em572_Reg.tiff": Vmt channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy4_CD44_Ex589_Em615_Reg.tiff": CD44 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy4_EZH2_Ex470_Em510_Reg.tiff": EZH2 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy4_H3K9ac_Ex650_Em676_Reg.tiff": H3K9ac channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy4_HP1_Ex405_Em438_Reg.tiff": HP1 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy4_P21_Ex530_Em572_Reg.tiff": P21 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy5_H3K4me3_Ex530_Em572_Reg.tiff": H3K4me3 channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy5_H3K27ac_Ex405_Em438_Reg.tiff": H3K27ac channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy5_RNAPII_Ex650_Em676_Reg.tiff": RNAPII channel of SW480 cells treated with 5-FU for 3 days. "SW480_5Fu_3d_Cy6_H3K27me3_Ex650_Em676_Reg.tiff": H3K27me3 channel of SW480 cells treated with 5-FU for 3 days. "SW480_Crl_Cy1_H3K27me3_Ex650_Em676_Reg.tiff": H3K27me3 channel of untreated SW480 cells. "SW480_Crl_Cy1_LMNAC_Ex530_Em572_Reg.tiff": LMNAC channel of untreated SW480 cells. "SW480_Crl_Cy2_CENPA_Ex650_Em676_Reg.tiff": CENPA channel of untreated SW480 cells. "SW480_Crl_Cy2_H3_Ex405_Em438_Reg.tiff": H3 channel of untreated SW480 cells. "SW480_Crl_Cy2_Ki67_Ex470_Em510_Reg.tiff": Ki67 channel of untreated SW480 cells. "SW480_Crl_Cy2_MCM7_Ex589_Em615_Reg.tiff": MCM7 channel of untreated SW480 cells. "SW480_Crl_Cy3_H2Ax_Ex589_Em615_Reg.tiff": H2Ax channel of untreated SW480 cells. "SW480_Crl_Cy3_H3K9me3_Ex650_Em676_Reg.tiff": H3K9me3 channel of untreated SW480 cells. "SW480_Crl_Cy3_P53_Ex470_Em510_Reg.tiff": P53 channel of untreated SW480 cells. "SW480_Crl_Cy3_Vmt_Ex530_Em572_Reg.tiff": Vmt channel of untreated SW480 cells. "SW480_Crl_Cy4_CD44_Ex589_Em615_Reg.tiff": CD44 channel of untreated SW480 cells. "SW480_Crl_Cy4_EZH2_Ex470_Em510_Reg.tiff": EZH2 channel of untreated SW480 cells. "SW480_Crl_Cy4_H3K9ac_Ex650_Em676_Reg.tiff": H3K9ac channel of untreated SW480 cells. "SW480_Crl_Cy4_HP1_Ex405_Em438_Reg.tiff": HP1 channel of untreated SW480 cells. "SW480_Crl_Cy4_P21_Ex530_Em572_Reg.tiff": P21 channel of untreated SW480 cells. "SW480_Crl_Cy5_H3K4me3_Ex530_Em572_Reg.tiff": H3K4me3 channel of untreated SW480 cells. "SW480_Crl_Cy5_H3K27ac_Ex405_Em438_Reg.tiff": H3K27ac channel of untreated SW480 cells. "SW480_Crl_Cy5_RNAPII_Ex650_Em676_Reg.tiff": RNAPII channel of untreated SW480 cells. "SW480_Crl_Cy6_H3K27me3_Ex650_Em676_Reg.tiff": H3K27me3 channel of untreated SW480 cells. **Folder: "Live Tracking QPI Video_Fig5,7,8"** This folder contains the label-free quantitative phase imaging (QPI) videos used in Figures 5, 7, and 8 of the main text. "SW480_Control.tif": label-free quantitative phase images (120 frames) of untreated SW480 cells. "SW480_5Fu_3day.tif": label-free quantitative phase images (120 frames) of SW480 cells treated with 5-FU for 3 days. **Folder: "Mesoscopic Expansion Image Stack"** This folder contains the three-dimensional fluorescence image stack used in Figure 9 of the main text. "expansion tissue 3D stack.tif": 3D image stack of the expanded colon tissue section. **Folder: "Live Tracking QPI Video_Fig3"** This folder contains the label-free quantitative phase imaging (QPI) videos used in Figure 3 of the main text. Subfolder "SW480_5Fu_Fig3" contains four QPI image stacks of SW480 cells treated with 5Fu: "SW480_5Fu_4h_Tp_ph_1registered.tif": contains the 1st to 30th frame "SW480_5Fu_4h_Tp_ph_2registered.tif": contains the 31th to 60th frame "SW480_5Fu_4h_Tp_ph_3registered.tif": contains the 61th to 90th frame "SW480_5Fu_4h_Tp_ph_4registered.tif": contains the 91th to 120th frame Subfolder "SW480_Crl_Fig3" contains four QPI image stacks of untreated SW480 cells: "SW480_Crl_4h_Tp_ph_1registered.tif": contains the 1st to 30th frame "SW480_Crl_4h_Tp_ph_2registered.tif": contains the 31th to 60th frame "SW480_Crl_4h_Tp_ph_3registered.tif": contains the 61th to 90th frame "SW480_Crl_4h_Tp_ph_4registered.tif": contains the 91th to 120th frame