DOI: 10.5061/dryad.mgqnk99b1
title: Data from: Label-free imaging of intracellular structures in living mammalian cells via external apodization phase-contrast microscopy

description: This dataset contains all raw and processed data supporting the findings
 of the associated research article. The data include quantitative
 measurements and imaging files (e.g., TIFF and CSV formats) obtained using
 ExAPC microscopy and fluorescence microscopy. The files are organized into
 folders corresponding to each figure in the manuscript, with clear
 subfolder structures distinguishing raw data, processed outputs, and
 numerical summaries. Each file is accompanied by a concise description
 detailing its type and analytical context. The dataset can be reused for
 validating the reported analyses, applying alternative image-processing or
 statistical approaches, or comparing intracellular structural features
 across different cell types or experimental conditions. All data are fully
 de-identified and derived from non-human cell lines; therefore, no ethical
 approval or informed consent was required.
description: # Data from: Label-free imaging of intracellular structures in living
 mammalian cells via external apodization phase-contrast microscopy ##
 **Figure 1** | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2
 Name** | **File Name** | **File Type** | **Description** | |
 :------------------- | :------------------- | :------------------- |
 :------------------------------------------------------------ |
 :------------ |
 :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 1 | Figure 1B | - | 20241113-#31 U2OS APC mio\_crop\_crop.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live A549 cells observed using ExAPC microscopy under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1B | - | 20241113-#31 U2OS DM mito\_crop\_crop.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live A549 cells observed using phase contrast microscopy under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1B | - | Figure 1B Line scan.csv | csv | This file contains line-scan data corresponding to Figure 1B. | | Figure 1 | Figure 1C | - | ExAPC Postion 1\_20241114-#3 Aastrocyte WT002 APC\_crop2.nd2 | nd2 | Representative microscopy image corresponding to Figure 1C. The image shows live primary astrocytes observed using ExAPC microscopy under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1C | - | ExAPC Postion 2\_20241114-#5 Aastrocyte WT002 APC\_crop3.nd2 | nd2 | Representative microscopy image corresponding to Figure 1C. The image shows live primary astrocytes observed using ExAPC microscopy under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1C | - | ODT Position 1\_20241114-#3 Aastrocyte WT002\_odt\_crop2.nd2 | nd2 | Representative microscopy image corresponding to Figure 1C. The image shows live primary astrocytes observed using ODT under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1C | - | ODT Position 2\_20241114-#5 Aastrocyte WT002\_odt\_crop06.nd2 | nd2 | Representative microscopy image corresponding to Figure 1C. The image shows live primary astrocytes observed using ODT under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1D | - | 20241114-#11 neuron WT002\_odt.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live primary neurons observed using ODT under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1D | - | 20241114-#11 neuron WT002\_odt\_crop.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live primary neurons observed using ODT under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1D | - | 20241114-#11 neuron WT002 ExAPC.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live primary neurons observed using ExAPC microscopy under the experimental conditions described in the manuscript. | | Figure 1 | Figure 1D | - | 20241114-#11 neuron WT002 ExAPC\_crop2.nd2 | nd2 | Representative microscopy image corresponding to Figure 1B. The image shows live primary neurons observed using ExAPC microscopy under the experimental conditions described in the manuscript. | ## Figure 2 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------------ | :------------------- | :---------------------------------------------------------------------------- | :------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 2 | ELL analysis | - | 20220720-#1 A549 20FPS-3\_crop ELS analysis.nd2 | nd2 | Representative ExAPC microscopy image. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2A Nucleus | - | 20220718-#3 A549 Hoechst\_crop\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2A. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2A Nucleus | - | 20220718-#3 A549 Hoechst\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2A. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2B Mitochondria | - | 20220718-#6 A549 mitoR\_crop2 - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2B. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2B Mitochondria | - | 20220718-#6 A549 mitoR\_crop2 - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2B. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2C Actin | - | 20220718-#21 A549 #196 Lifeact-YFP\_crop - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2C. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2C Actin | - | 20220718-#21 A549 #196 Lifeact-YFP\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2C. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2D ER | - | 20220718-#15 A549 #170 YFP-Cb5\_crop - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2D. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2D ER | - | 20220718-#15 A549 #170 YFP-Cb5\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2D. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2E Endosome | - | 20241014-#2 A549 ECG - Clarified.nd2 - Denoised\_crop\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2E. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2E Endosome | - | 20241014-#2 A549 ECG - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2E. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2F Lysosome | - | 20220722-#1 A549 lysotracker\_crop - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2F. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2F Lysosome | - | 20220722-#1 A549 lysotracker\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2F. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2G Golgi apparatus | - | 20220718-#18 A549 #171 YFP-giantin\_crop - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2G. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | Figure 2G Golgi apparatus | - | 20220718-#18 A549 #171 YFP-giantin\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 2G. The image shows live A549 cells under the experimental conditions described in the manuscript. | | Figure 2 | - | - | Figure 2\_1\_Nucleus.csv | csv | This file contains line-scan data corresponding to Figure 2A. | | Figure 2 | - | - | Figure 2\_2\_Mitochondria.csv | csv | This file contains line-scan data corresponding to Figure 2B. | | Figure 2 | - | - | Figure 2\_3\_Actin.csv | csv | This file contains line-scan data corresponding to Figure 2C. | | Figure 2 | - | - | Figure 2\_4\_ER.csv | csv | This file contains line-scan data corresponding to Figure 2D. | | Figure 2 | - | - | Figure 2\_5\_Endosome.csv | csv | This file contains line-scan data corresponding to Figure 2E. | | Figure 2 | - | - | Figure 2\_6\_Lysosome.csv | csv | This file contains line-scan data corresponding to Figure 2F. | | Figure 2 | - | - | Figure 2\_7\_Golgi.csv | csv | This file contains line-scan data corresponding to Figure 2G. | | Figure 2 | - | - | Figure 2\_8\_Endosome-like size.csv | csv | This file contains quantitative data used to calculate the average size of ELLs. | ## Figure 3 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :-------------------------------------------------------------- | :------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 3 | 1. HeLa | - | 20230717-#14 HeLa\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 3 | 1. HeLa | - | 20230717-#14 HeLa\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 3 | 2. HCT116 | - | 20230717-#17 HCT116\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live HCT116 cells under the experimental conditions described in the manuscript. | | Figure 3 | 2. HCT116 | - | 20230717-#17 HCT116\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live HCT116 cells under the experimental conditions described in the manuscript. | | Figure 3 | 3. Hep3B | - | 20230717-#2 Hep3B\_crop - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 3 | 3. Hep3B | - | 20230717-#2 Hep3B\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 3 | 4. MDA-MB-231 | - | 20230717-#24 MDA-MB-231\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live MDA-MB-231 cells under the experimental conditions described in the manuscript. | | Figure 3 | 4. MDA-MB-231 | - | 20230717-#24 MDA-MB-231\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live MDA-MB-231 cells under the experimental conditions described in the manuscript. | | Figure 3 | 5. U2OS | - | 20230717-#12 U2OS\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live U2OS cells under the experimental conditions described in the manuscript. | | Figure 3 | 5. U2OS | - | 20230717-#12 U2OS\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live U2OS cells under the experimental conditions described in the manuscript. | | Figure 3 | 6. NIH-3T3 | - | 20230717-#7 NIH-3T3\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live NIH-3T3 cells under the experimental conditions described in the manuscript. | | Figure 3 | 6. NIH-3T3 | - | 20230717-#7 NIH-3T3\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 3. The image shows live NIH-3T3 cells under the experimental conditions described in the manuscript. | ## Figure 4 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :--------------------------- | :------------------- | :--------------------------------------------------------------------- | :------------ | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 4 | Figure 4A Cell division | 1. HeLa cells | 20220726-#7 HeLa 1min long time-lapse\_crop 1\_short version\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 4A. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4A Cell division | 1. HeLa cells | 20220726-#7 HeLa 1min long time-lapse\_crop 1\_short version.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 4A. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4A Cell division | 2. hiPS cells | 20220904 hiPSC Day3 1FPM 36h\_crop\_F1-317.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 4A. The image shows live hiPS cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4A Cell division | 2. hiPS cells | 20220904 hiPSC Day3 1FPM 36h\_crop\_crop\_F1-317.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 4A. The image shows live hiPS cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4B Apoptosis | - | 20220705 HeLa 2ul STS\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 4B. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4C Entosis | - | 20220906-#2 ZR 1FPM 16h\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 4C. The image shows live ZR75-1 cells under the experimental conditions described in the manuscript. | | Figure 4 | Figure 4D Entotic cell death | - | 20220923 ZR75 continued\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 4D. The image shows live ZR75-1 cells under the experimental conditions described in the manuscript. | ## Figure 5 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :------------------------------------------------------------- | :------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 5 | Figure 5A | - | (UpperLEFT) 20230717-#17 HeLa 1FPS 1min for zstack\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5A. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5A | - | (Others) 20230717-#17 HeLa 1FPS zstack1\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5A. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5C | - | 20230717-#15 HeLa 1FPS 30min\_crop\_crop\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5C. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5D | - | 20220902-#1 HeLa 5% 1,6-HD\_crop\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5D. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5D | - | 20220902-#1 HeLa 5% 1,6-HD\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5D. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5E | - | 20220912-#4 HeLa 100 mM Add frame 2 time-lapse\_crop\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | Figure 5E | - | 20220912-#4 HeLa 100 mM Add frame 2 time-lapse\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 5E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 5 | - | - | Figure 5 Manuscript.csv | csv | This file contains numerical data used to calculate the percentage of HeLa cells exhibiting BCLs, as shown in Figure 5A. | | Figure 5 | - | - | Figure 5B.csv | csv | This file contains numerical data corresponding to Figure 5B. | | Figure 5 | - | - | Figure 5F.csv | csv | This file contains numerical data corresponding to Figure 5F. | | Figure 5 | - | - | Figure 5G.csv | csv | This file contains numerical data corresponding to Figure 5G. | ## Figure 6 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :------------------------------------------------------------------------------------------- | :------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | Figure 6 | Figure 6A | - | 20230722-#1 U2OS GFP-IRS1-3 - Clarified.nd2 - Denoised\_crop\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6A. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6A | - | 20230722-#1 U2OS GFP-IRS1-3 - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6A. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6B | - | 20230720-#2 U2OS GFP-IRS1 1FPM 1h\_crop - Clarified. - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6B. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6J | - | 20230720-#3 U2OS GFP-IRS1 1FPS-1\_crop\_cropFig - Clarified.nd2 - Denoised\_crop05.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6J. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6J | - | 20230720-#3 U2OS GFP-IRS1 1FPS-1\_crop\_cropFig - Clarified.nd2 - Denoised\_crop ROI#1.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6J. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6J | - | 20230720-#3 U2OS GFP-IRS1 1FPS-1\_crop\_cropFig - Clarified.nd2 - Denoised\_crop01 ROI#3.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6J. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6J | - | 20230720-#3 U2OS GFP-IRS1 1FPS-1\_crop\_cropFig - Clarified.nd2 - Denoised\_crop02 ROI#2.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6J. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | Figure 6K | - | Kymograph.nd2 | nd2 | Kymograph corresponding to Figure 6K, showing the interaction between IRS-1 droplets and ELLs. | | Figure 6 | Figure 6K | - | 20230720-#3 U2OS GFP-IRS1 1FPS-1\_crop\_cropKymograph2.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 6K. The image shows live U-2OS cells expressing GFP-tagged IRS1 under the experimental conditions described in the manuscript. | | Figure 6 | - | - | Figure 6A.csv | csv | This file contains numerical data corresponding to Figure 6A. | | Figure 6 | - | - | Figure 6C,D.csv | csv | This file contains numerical data corresponding to Figure 6C and 6D. | | Figure 6 | - | - | Figure 6E.csv | csv | This file contains numerical data corresponding to Figure 6E. | | Figure 6 | - | - | Figure 6F.csv | csv | This file contains numerical data corresponding to Figure 6F. | | Figure 6 | - | - | Figure 6G.csv | csv | This file contains numerical data corresponding to Figure 6G. | | Figure 6 | - | - | Figure 6H.csv | csv | This file contains numerical data corresponding to Figure 6H. | | Figure 6 | - | - | Figure 6I.csv | csv | This file contains numerical data corresponding to Figure 6I. | ## Figure 7 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :----------------------------------------------------------------------------------- | :------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 7 | Figure 7B | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified.nd2 - Denoised\_F1-550.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7B. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7B | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified.nd2 - Denoised\_crop\_F1-550.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7B. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7C | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop F25 patternwhite.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 7C. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7C | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop F7 patternb.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 7C. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7E | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised2\_crop02 (ROI#2).nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7E | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised2.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7E | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised2\_crop (ROI#1).nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7E | - | 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised2\_crop01 (ROI#3).nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 7E. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7F | - | 20230812-#2 HeLa OA LipiBlueZ1\_crop04 (Pos#3).nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 7F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7F | - | 20230812-#2 HeLa OA LipiBlueZ1\_crop01 (Pos#2).nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 7F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | Figure 7F | - | 20230812-#2 HeLa OA LipiBlueZ1\_crop03 (Pos#1).nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 7F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 7 | - | - | Figure 7D.csv | csv | This file contains numerical data corresponding to Figure 7D. | ## Figure 8 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :-------------------------------------------------------------------------------------------------------------- | :------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 8 | Figure 8F | - | Nuclear membrane 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised Cell#1 Summary2\_crop F603.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 8F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 8 | Figure 8F | - | ELLs 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised Cell#2 Summary\_crop F877.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 8F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 8 | Figure 8F | - | Lipid droplet 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised Cell#1 Summary2\_crop F730.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 8F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 8 | Figure 8F | - | Mitochondria 20220925-#1 HeLa 100ulOA lipiBlue\_crop - Clarified. - Denoised Cell#2 Summary\_crop F266.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 8F. The image shows live HeLa cells under the experimental conditions described in the manuscript. | | Figure 8 | - | - | Figure 8B.csv | csv | This file contains numerical data corresponding to Figure 8B. | | Figure 8 | - | - | Figure 8C.csv | csv | This file contains numerical data corresponding to Figure 8C. | | Figure 8 | - | - | Figure 8D.csv | csv | This file contains numerical data corresponding to Figure 8D. | | Figure 8 | - | - | Figure 8E.csv | csv | This file contains numerical data corresponding to Figure 8E. | | Figure 8 | - | - | Figure 8G.csv | csv | This file contains numerical data corresponding to Figure 8G. | | Figure 8 | - | - | Figure 8H.csv | csv | This file contains numerical data corresponding to Figure 8H. | | Figure 8 | - | - | Figure 8I.csv | csv | This file contains numerical data corresponding to Figure 8I. | | Figure 8 | - | - | Figure 8J.csv | csv | This file contains numerical data corresponding to Figure 8J. | ## Figure 9 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :----------------------------------------------------------------------- | :------------ | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 9 | Figure 9A | - | 20241007-#1 Hep3B NO mitoR\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 9A. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 9 | Figure 9A | - | 20241007-#1 Hep3B mitoR - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 9A. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 9 | Figure 9B | - | 20230119-#4 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_crop01.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 9B. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | ## Figure 10 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :---------------------------------------------------------------------------------------------- | :------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F10.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F10-2.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F1084.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F1173.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F1332.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F14.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F1704.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F218.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F303.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F305.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F514.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F578.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F602.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F698.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F733.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F775.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F859.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10A | - | 20230119-#4 Hep3B mitoR 1PS 30min F986.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before division, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10B | - | 20230119-#2 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_cropF570\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 10B. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1051.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1213.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1377.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1407.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1474.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1475.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F1513.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F380.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F484.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F518.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F544.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F648.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F698.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F743.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F748.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10E | - | 20230119-#2 Hep3B mitoR 1PS 30min F952.tif | tif | One of the gallery images showing a mitochondrion in Hep3B cells one frame before fusion, derived from a binarized image obtained by ExAPC microscopy. | | Figure 10 | Figure 10F | - | 20230119-#4 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_F936crop\_crop (End-to-End).nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 10F. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 10 | Figure 10F | - | 20230119-#4 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_cropF1308\_crop (End-to-Side).nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 10F. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 10 | - | - | Figure 10C,D.csv | csv | This file contains numerical data corresponding to Figure 10C and 10D. | | Figure 10 | - | - | Figure 10G,H.csv | csv | This file contains numerical data corresponding to Figure 10G and 10H. | ## Figure 11 | **Main folder Name** | **Subfolder#1 Name** | **Subfolder#2 Name** | **File Name** | **File Type** | **Description** | | :------------------- | :------------------- | :------------------- | :------------------------------------------------------------------------------- | :------------ | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | Figure 11 | Figure 11A | - | 20230812-#2 Hep3B TMRM No FCCP\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11A. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11A | - | 20230812-#1 Hep3B TMRM 40uM FCCP\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11A. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11B | - | 20230810-#3 Hep3B 40uM FCCP\_crop\_crop for movie.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11B. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11B | - | 20230810-#2 Hep3B Before\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11B. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11C | - | 40uM FCCP 20230822-#4 U2OS 40uM FCCP\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11C. The image shows live U-2 OS cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11C | - | 0uM FCCP 20230822-#2 U2OS Control\_crop - Clarified.nd2 - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11C. The image shows live U-2 OS cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11D | - | 20230820-#2 U2OS 40uM FCCP\_crop for movie.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11D. The image shows live U-2 OS cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11D | - | 20230820-#1 U2OS Before\_crop - Clarified. - Denoised.nd2 | nd2 | Representative ExAPC and fluorescence microscopy image corresponding to Figure 11D. The image shows live U-2 OS cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11E | - | 40uM FCCP 20230810-#3 Hep3B 40uM FCCP\_crop\_crop\_crop\_1201-1228.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11E. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11E | - | 0uM FCCP 20230119-#4 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11E. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11F | - | 40uM FCCP 20230810-#3 Hep3B 40uM FCCP\_crop\_crop\_crop\_1201-1228.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11F. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | Figure 11F | - | 0 uM FCCP 20230119-#4 Hep3B mitoR 1PS 30min - Clarified.nd2 - Denoised\_crop.nd2 | nd2 | Representative ExAPC microscopy image corresponding to Figure 11F. The image shows live Hep3B cells under the experimental conditions described in the manuscript. | | Figure 11 | - | - | Figure 11A.csv | csv | This file contains numerical data corresponding to Figure 11A. | | Figure 11 | - | - | Figure 11C.csv | csv | This file contains numerical data corresponding to Figure 11C. | ## Description of the data and file structure ## **Files and variables** #### File: 20251020_ExAPC_DRYAD_Final.zip **Description:** See Data description ## Code/software **[Software]** NIS-Elements Microsoft Excel