An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization
Data files
Sep 24, 2024 version files 57.37 GB
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Omni_Mesoscope_data.zip
57.37 GB
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README.md
5.77 KB
Abstract
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.
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
- Ma, Hongqiang et al. (2024), An Omni-Mesoscope for multiscale high-throughput quantitative phase imaging of cellular dynamics and high-content molecular characterization, [], Posted-content, https://doi.org/10.1101/2024.07.18.604137
