Data from: Label-free imaging of intracellular structures in living mammalian cells via external apodization phase-contrast microscopy

Ohno, Hiroshi1; Nishimura, Takenori2; Kainoh, Kenta1; Ohashi, Yoshitaka1; Onodera, Naoko1; Kano, Mayuko1; Sari, Lay Nurhana1; Masuda, Masato3; Tamura, Yoshiaki3; Nishino, Teppei1; Hayashi, Yusuke4; Yamamoto, Yusuke4; Takahashi, Shin-Ichiro2; Mishima, Yuta1; Yoneyama, Yosuke5; Takeuchi, Yoshinori1; Sekiya, Motohiro1; Matsuzaka, Takashi1; Miyamoto, Takafumi 1 ; Shimano, Hitoshi1

Published Oct 22, 2025 on Dryad. https://doi.org/10.5061/dryad.mgqnk99b1

Data files

Oct 22, 2025 version files 17.47 GB

20251020_ExAPC_DRYAD_Final.zip

17.47 GB
README.md

64.62 KB

Abstract

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.

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