Image repository from : Subcellular nanoparticle trafficking investigated with label-free, live cell imaging
Data files
Apr 14, 2026 version files 7.84 GB
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2.5um-LOX-20um-every40slidse.tif
2.73 MB
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2.5um-LOX-20um-every60slides.tif
2.18 MB
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250um-LOX-20um-every40slidse.tif
2.73 MB
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250um-LOX-20um-every60slides.tif
2.18 MB
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cannibalism-T47D-SLCKO-20um.tif
19.37 MB
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FreeDox-LOX-cells-moving-20um-bendta.tif
100.20 MB
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Group_1_wellA1_RI_MIP_FITC_Cy5_1_52_8bit_stitched-1.tif
12.20 MB
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HA_LbLDoxil_RImovie_hours_25um.tif
1.87 GB
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HA-LbL-Doxil-RI-25hours-20um-crop.tif
347.51 MB
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HA-LbL-Doxil-RI-hours-20um-movie.tif
1.87 GB
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HA-LbL-Parental-dead-20um.tif
1.73 MB
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HA-LbL-Parental-mixed-dead-20um-scale.tif
1.90 MB
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HA-LbL-Parental-very-dead-20um.tif
6.07 MB
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LOX-freeDox-001-death-6xMontage-20um-bendta.tif
3.28 MB
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LOX-freeDox-grid8-death-5xMontage-20um-over20hrs.tif
1.44 MB
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LOX-freeDox-grid9-death-6xMontage-20um-timestamp.tif
1.72 MB
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LOX-LUC-OE-LNP001-photobleach-20um-RI-Cy5-only.tif
64.40 MB
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LOX-LUC-OE-LNP001-photobleach-20um.tif
96.60 MB
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LOX-Parental-Doxil-002-FreeDoxo-20um.tif
1.76 GB
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LOX-Parental-Doxil-002-grid3-20um-dyingcells-timestamp.tif
308.38 MB
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LOX-Parental-Doxil-002-grid3-20um-dyingcells.tif
308.38 MB
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LOX-Parental-Doxil-002-grid8-20um-dyingcells.tif
308.36 MB
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LOX-Parental-Doxil-002-grid9-20um-dyingcells-timestamp.tif
308.37 MB
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LOX-Parental-FreeDoxo-20um-deadcells.tif
4.59 MB
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LOX-SLC-OE-LNP002-Crop-20um-8fps.tif
56.49 MB
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LUC_OE_3D_cy5_t_24_002.tif
262.67 KB
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LUC_OE_mitosis_10um.tif
3.29 MB
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LUC_OE_wellD3_RI_20um_edit.tif
2.82 MB
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LUC-OE_UT_mitosis_and_death_cropped_10um.tif
25.16 MB
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LUC-OE_UT_mitosis_and_death_cropped.tif
25.16 MB
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macropino-Montage-1.tif
9.73 MB
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macropino-Montage-2.tif
9.73 MB
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merge_A1_LOX_PS_bare_20um.tif
668.04 KB
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Mitosis-LUC-OE-10um-Montage.tif
263.96 KB
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Montage-6x-DOX002-Doxil.tif
13.11 MB
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Montage-6x-DOX002-FreeDox.tif
9.91 MB
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Montage-6x-DOX002-HA.tif
13.11 MB
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Montage-6x-DOX002-PLE.tif
13.11 MB
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Montage-6x-DOX002-Untreated.tif
3.28 MB
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Montage1-T47D-LNP-20um.tif
195.67 KB
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Montage2-T47D-LNP-20um.tif
64.55 KB
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Montage3-T47D-LNP-20um.tif
66.10 KB
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Montage4-T47D-LNP-20um.tif
66.10 KB
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Montage5-T47D-SLCKO-LNP-20um.tif
364.48 KB
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Montage6-T47D-SLCKO-LNP-20um.tif
120.61 KB
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Montage7-T47D-SLCKO-LNP-20um.tif
122.16 KB
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Montage8-T47D-SLCKO-LNP-20um.tif
122.37 KB
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new_stack.tif
1.07 MB
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old-bare-lipo-control-24hr-merge.tif
528.28 KB
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old-bare-lipo-control-24hr.tif
525.07 KB
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PS-bare-merge-Group_1_wellA1_RI_MIP_FITC_Cy5_1_52_8bit_stitched-1-1.tif
669.38 KB
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README.md
12.56 KB
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SKNBE2-PRRX1-cell-10um.tif
524.92 KB
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SKNBE2-PRRX1-mitosis-8fps-10um.tif
8.14 MB
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SLC_KO_F5_wellG8_RI_20um_edit.tif
2.82 MB
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SLC_OE_wellB8_RI_20um_edit.tif
2.82 MB
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SLC_OE_wellB8_RI_20um.tif
2.82 MB
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SLC-OE-LNP-002-after-5hr.tif
5.70 MB
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SLC-OE-UT-cells-20um.tif
7.91 MB
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T47D-SLCKO-F5-macropino-magenta-20um.tif
6.80 MB
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T47D-SLCKO-LNP002-merge-macro-8fps-20um-11hours.tif
54.38 MB
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T47D-SLCKO-LNP002-merge-macro-8fps-20um.tif
54.38 MB
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T47D-SLCKO-Merged-macropino-20um.tif
13.09 MB
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UT-slide16.tif
6.07 MB
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UT-slide199.tif
6.07 MB
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VG-Dend-PolyIC-NP-macs-10um.tif
267.76 KB
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vyxeos-16hr-UTvs250um-Combined_Stacks.tif
24.29 MB
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vyxeos-250um-16hr-CombinedStacks.tif
12.14 MB
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vyxeos-250um-slide16.tif
6.07 MB
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vyxeos-250um-slide199.tif
6.07 MB
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vyxeos-UT-16hr-CombinedStacks.tif
12.14 MB
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WT_wellF3_RI_20um_edit.tif
2.82 MB
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WT_wellF3_RI_20um.tif
2.82 MB
Abstract
Nanoparticle drug delivery systems have significant potential to transform precision medicine due to their ability to encapsulate a wide range of cargos that can be packaged in various types of carriers. Delivery kinetics can also be modified by altering the surface chemistry of the nanoparticle carrier. However, a gap remains in our understanding of the cellular mechanisms underlying nanoparticle uptake and subcellular trafficking kinetics. A comprehensive understanding of nanoparticle-cell interactions considering both the nanocarrier and the drug cargo has been challenging, partly due to technological limitations. Here, we present a robust long-term imaging workflow as a novel tool to study live-cell dynamics and nanoparticle delivery. We show how the integration of holography, tomography, and fluorescence microscopy enhances the capacity to study living, adherent cells in vitro label-free with further applications in assessing nanoparticle uptake and delivery kinetics over time.
We also introduce a method of characterizing kinetic data from a library of lipid- and polymer-based nanoformulations without the need for cellular labels. This application of dynamic fluorescent holotomography as a new method to investigate nanoparticle uptake and cargo delivery highlights the expanding utility of multimodal, label-free, live imaging techniques.
Dataset DOI: 10.5061/dryad.zkh1893qf
Description of the data and file structure
The contents of this Dryad dataset include all the acquisition files, edited montages generated using ImageJ, auto-adjusted processed acquisitions with added scale bars, and the metadata cell sheet, which describes the acquisition parameters set for the corresponding data file.
The files are all TIFF files. These data are titled to indicate as much detail as necessary to identify the file. This includes: the format of the image (movie, still, Combined Stack, Merged, or montage), the cell line type (SKNBE2, T47D, or LOXIMVI as “LOX”), the treatment type (bare liposomes, LNPs, UT=Untreated, Doxil, or free dox[orubicin]), the durations (in hours) and/or what the scale bar is in microns (“um”). Further information in the titles may include the trial number (i.e. “001” or “002”) or the cell line delineation, which for LOXIMVI are Parental, Control LUC OE, or SLC OE; for T47D are Control or SLC KO; and for SKNBE2 are Parental or PRRX1. For acquisitions performed in a 96-well plate, there are specific grid numbers included in the data title that arbitrarily indicate the grid number of interest for that image. Similarly, the slide number is identified in some data. Lastly, some titles include the observation of interest, such as “mitosis,” “death,” or “macro,” for macropinocytosis. Data is not available for reuse without permission from the corresponding author.
The raw data is processed immediately after acquisition using the Nanolive SA proprietary feature, STEVE. In this code, the 96-stacks are combined per slide (between 50-350 slides per acquisition). This file is then used to process the maximum-intensity projection in ImageJ. All post-processing is automatically saved in stages to be able to view any slide or stack of choice throughout the acquisition. These data are not available in Dryad due to the large file sizes. All images were processed using ImageJ (aka FIJI).
MICROSCOPY: Cells were imaged in a humidified, temperature-controlled chamber incubator (Tokai Hit) maintained at 37C with 5% CO2 supply. Temperature stabilization for 10-30 minutes is necessary to avoid fog interference before acquiring images. All images and movies were acquired on the 3D Cell Explorer 96focus microscope (Nanolive SA, Switzerland). Acquisitions using fluorescence were captured with filters for FITC or Cy5. Detailed acquisition parameters and experimental conditions can be found in the table below.
Files and variables
File: 2.5um-LOX-20um-every40slidse.tif
Description:
File: 250um-LOX-20um-every40slidse.tif
Description:
File: 250um-LOX-20um-every60slides.tif
Description:
File: 2.5um-LOX-20um-every60slides.tif
Description:
File: cannibalism-T47D-SLCKO-20um.tif
Description:
File: HA-LbL-Parental-mixed-dead-20um-scale.tif
Description:
File: HA-LbL-Parental-dead-20um.tif
Description:
File: LOX-freeDox-001-death-6xMontage-20um-bendta.tif
Description:
File: Group_1_wellA1_RI_MIP_FITC_Cy5_1_52_8bit_stitched-1.tif
Description:
File: HA-LbL-Parental-very-dead-20um.tif
Description:
File: LOX-freeDox-grid9-death-6xMontage-20um-timestamp.tif
Description:
File: LOX-freeDox-grid8-death-5xMontage-20um-over20hrs.tif
Description:
File: FreeDox-LOX-cells-moving-20um-bendta.tif
Description:
File: LOX-Parental-FreeDoxo-20um-deadcells.tif
Description:
File: LOX-LUC-OE-LNP001-photobleach-20um-RI-Cy5-only.tif
Description:
File: LUC_OE_3D_cy5_t_24_002.tif
Description:
File: LUC_OE_mitosis_10um.tif
Description:
File: LOX-SLC-OE-LNP002-Crop-20um-8fps.tif
Description:
File: LUC_OE_wellD3_RI_20um_edit.tif
Description:
File: LOX-LUC-OE-LNP001-photobleach-20um.tif
Description:
File: HA-LbL-Doxil-RI-25hours-20um-crop.tif
Description:
File: HA_LbLDoxil_RImovie_hours_25um.tif
Description:
File: macropino-Montage-1.tif
Description:
File: LUC-OE_UT_mitosis_and_death_cropped_10um.tif
Description:
File: macropino-Montage-2.tif
Description:
File: LUC-OE_UT_mitosis_and_death_cropped.tif
Description:
File: HA-LbL-Doxil-RI-hours-20um-movie.tif
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File: merge_A1_LOX_PS_bare_20um.tif
Description:
File: Mitosis-LUC-OE-10um-Montage.tif
Description:
File: LOX-Parental-Doxil-002-grid3-20um-dyingcells-timestamp.tif
Description:
File: LOX-Parental-Doxil-002-grid3-20um-dyingcells.tif
Description:
File: Montage-6x-DOX002-FreeDox.tif
Description:
File: Montage-6x-DOX002-Doxil.tif
Description:
File: LOX-Parental-Doxil-002-grid9-20um-dyingcells-timestamp.tif
Description:
File: Montage4-T47D-LNP-20um.tif
Description:
File: Montage-6x-DOX002-Untreated.tif
Description:
File: Montage2-T47D-LNP-20um.tif
Description:
File: Montage3-T47D-LNP-20um.tif
Description:
File: Montage6-T47D-SLCKO-LNP-20um.tif
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File: Montage5-T47D-SLCKO-LNP-20um.tif
Description:
File: Montage8-T47D-SLCKO-LNP-20um.tif
Description:
File: Montage-6x-DOX002-HA.tif
Description:
File: PS-bare-merge-Group_1_wellA1_RI_MIP_FITC_Cy5_1_52_8bit_stitched-1-1.tif
Description:
File: SKNBE2-PRRX1-cell-10um.tif
Description:
File: Montage1-T47D-LNP-20um.tif
Description:
File: Montage7-T47D-SLCKO-LNP-20um.tif
Description:
File: new_stack.tif
Description:
File: old-bare-lipo-control-24hr-merge.tif
Description:
File: LOX-Parental-Doxil-002-grid8-20um-dyingcells.tif
Description:
File: SLC_KO_F5_wellG8_RI_20um_edit.tif
Description:
File: old-bare-lipo-control-24hr.tif
Description:
File: SLC_OE_wellB8_RI_20um.tif
Description:
File: SLC_OE_wellB8_RI_20um_edit.tif
Description:
File: Montage-6x-DOX002-PLE.tif
Description:
File: LOX-Parental-Doxil-002-FreeDoxo-20um.tif
Description:
File: VG-Dend-PolyIC-NP-macs-10um.tif
Description:
File: WT_wellF3_RI_20um.tif
Description:
File: WT_wellF3_RI_20um_edit.tif
Description:
File: T47D-SLCKO-F5-macropino-magenta-20um.tif
Description:
File: SLC-OE-LNP-002-after-5hr.tif
Description:
File: SKNBE2-PRRX1-mitosis-8fps-10um.tif
Description:
File: vyxeos-250um-slide16.tif
Description:
File: UT-slide16.tif
Description:
File: SLC-OE-UT-cells-20um.tif
Description:
File: UT-slide199.tif
Description:
File: vyxeos-250um-16hr-CombinedStacks.tif
Description:
File: vyxeos-250um-slide199.tif
Description:
File: vyxeos-16hr-UTvs250um-Combined_Stacks.tif
Description:
File: vyxeos-UT-16hr-CombinedStacks.tif
Description:
File: T47D-SLCKO-LNP002-merge-macro-8fps-20um-11hours.tif
Description:
File: T47D-SLCKO-LNP002-merge-macro-8fps-20um.tif
Description:
File: T47D-SLCKO-Merged-macropino-20um.tif
Description:
| CY5 | FITC | ||||||||||||
| Date | Experiment NP | Cell type(s) | Total duration (hr) | Grid scan | RI every X min | Fluo every X min | Power | Exposure (ms) | Gain | Power | Exposure (ms) | Gain | EVE analysis performed |
| 4/30/24 | Cy5 LNPs containing GFP mRNA | LOX IMVI | 20 | 4x4 | 8 | 8 | 12% | 80 | 50 | 8% | 75 | 30 | Cytotoxicity assay |
| T47D | |||||||||||||
| 5/9/24 | Carboxylated PS NPs and Cy5 bare liposomes | LOX IMVI | 16 | 1x1 | 12 | 12 | 10% | 80 | 50 | 8% | 50 | 15 | Cytotoxicity assay |
| T47D | |||||||||||||
| 5/22/24 | UT and Cy5 LNPs containing GFP mRNA | LOX IMVI | 24 | 4x4 | 7 | 7 | 10% | 100 | 30 | 12% | 150 | 35 | Cytotoxicity and Lipid droplet assays |
| 6/25/24 | Doxorubicin-loaded NPs | LOX IMVI | 35 | 3x3 | 5 | - | |||||||
| 6/27/24 | CPX-351 (VYXEOS) | LOX IMVI | 30 | 3x3 | 5 | - | |||||||
| 5/15/24 | Free PIC (Cy5) and PIC NPs (FITC) | DCs | 5 | 3x3 | 10 | 10 | 15% | 100 | 40 | 10% | 100 | 40 | |
| 6/5/24 | first 3 hours | DCs | 3 | 4x4 | 6 | 6 | 15% | 100 | 30 | 5% | 75 | 25 | |
| 6/5/24 | 20 hours | DCs | 18 | 4x4 | 8 | 8 | 15% | 120 | 30 | 7% | 75 | 25 |
Code/software
IMAGE ANALYSIS AND FIJI PROCESSING: Grid scan stitching was performed automatically using Nanolive SA proprietary analysis software (EVE). Automated analysis programs (LIVE Cytotoxicity Assay, LIVE Cell Death Assay, or the SMART Lipid Droplet Assay LIVE (all Nanolive SA)) were applied to the raw imaging data for automated segmentation and quantification of cells and lipid droplets, and for automated classification of cells into living, apoptotic, or necrotic states. All movies with fluorescent channels were processed in FIJI using Combine Stacks. For visualization after analysis, fluorescence and brightfield refractive index images were auto-adjusted for brightness and contrast.
The raw data is processed immediately after acquisition using the Nanolive SA proprietary feature, STEVE. In this code, the 96-stacks are combined per slide (between 50-350 slides per acquisition). This file is then used to process the maximum-intensity projection in ImageJ. All post-processing is automatically saved in stages to be able to view any slide or stack of choice throughout the acquisition. These data are not available in Dryad due to the large file sizes. All images were processed using ImageJ (aka FIJI).
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
