cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0xg9rbn
title: CIL: 54884. In Cell Image Library

description: ih-MSCs were cultured in a rotating wall vessel (RWV) bioreactor (RCCS-8DQ bioreactor (Synthecon, Houston, TX) fitted with 10 mL high aspect ratio vessels on custom-fabricated 120 ± 6.2 μm diameter gelMA microcarriers. For this purpose, approximately 110,000 gelMA microcarriers with a combined growth area of 50 cm2 and 5×104 cells (1000 cells/cm2) were incubated in 10 mL of CCM in the RWV bioreactor at 24 revolutions per minute. Half of the media was replaced with fresh CCM every 2 days. iH-MSCs fixed with 4% paraformaldehyde and fluorescently labeled with CellTracker Green (green), DRAQ-5 (blue), and DiI (gold) in the cytoplasm, nuclei, and plasma membrane, respectively. Label-free elastic scattering (white) and trasmitted light (grey) are also used to visualize the sample.

Passage 4 day 7 aggregate imaged with elastic scattering contrast and illuminated with 638 nm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
description: Imaging mode: Zeiss Z.1 Lightsheet microscope (fluorescence and scattering)
Visualization methods: FIJI/ImageJ
description: The adoption of cell-based therapies into the clinic will require tremendous large-scale expansion to satisfy future demand, and bioreactor-microcarrier cultures are best suited to meet this challenge. A robust optical imaging and image-analysis assay to non-destructively quantify cell number and cell volume was developed using fluorescence and elastic scattering contrast. This assay was successfully applied to monitor cellular growth of induced pluripotent derived mesenchymal stem cells (iH-MSCs) attached to spherical hydrogel microcarriers over time. Elastic scattering and fluorescence lightsheet microscopy were used to quantify cell volume and cell number at varying spatial scales. The fluorescence-based assay is used as ground truth data to correlate the elastic scattering-based assay data.

Fig3d Fixed passage 4 day 7 ih-MSc microcarrier aggreagate.
DOI: 10.6075/j02807tg
title: CIL: 54847, Danio rerio, Whole larva. In Cell Image Library

description: Sagittal sections of 5 days post-fertilization drl:APEX2-mCherry+ zebrafish larva in the region of the anterior kidney (eLife Table 1: APEX2 #1 5 dpf).
description: Imaging mode: SBEM
description: Larvae preparation for APEX2+;mCherry+ CLEM (eLife: Workflow #1). 5 dpf zebrafish larvae were prepared for MicroCT and SBEM as previously described (Deerinck et al., 2010). Briefly, immediately after light sheet imaging, larvae were fixed in 2.5% glutaraldehyde and 4% paraformaldehyde in 0.15 M cacodylate buffer (CB, pH 7.4) at 4°C overnight. After removing the fixative, larvae were treated for 15 minutes with 20 mM glycine in 0.15M CB, on ice to quench the unreacted glutaraldehyde. Preincubation was done in 2.5 mM DAB solution (25.24 mM stock in 0.1 M HCl) in 0.15 M CB for 1 hour on ice. For staining, 0.03% H2O2 containing DAB solution was added to the larvae on ice. The reaction was monitored every 5-10 minutes and stopped when the desired intensity was achieved. The staining buffer was washed off with 5x washes using 0.15 M CB. Then, larvae were washed with 0.15 M CB and then placed into 2% OsO4/1.5% potassium ferrocyanide in 0.15 M CB containing 2 mM CaCl2. The larvae were left for 30 min on ice and then 30 min at room temperature (RT). After thorough washing in double distilled water (ddH2O), larvae were placed into 0.05% thiocarbohydrazide for 30 min. Larvae were again washed and then stained with 2% aqueous OsO4 for 30 min. Larvae were washed and then placed into 2% aqueous uranyl acetate overnight at 4°C. Larvae were washed with ddH2O at RT and then stained with 0.05% en bloc lead aspartate for 30 min at 60°C. Larvae were washed with ddH2O and then dehydrated on ice in 50%, 70%, 90%, 100%, 100% ethanol solutions for 10 min at each step. Larvae were then washed twice with dry acetone and placed into 50:50 Durcupan ACM:acetone overnight. Larvae were transferred to 100% Durcupan resin overnight. Larvae were then flat embedded between glass slides coated with mould-release compound and left in an oven at 60°C for 72 h. The larva block was imaged with a Merlin scanning electron microscope equipped with a 3View2XP and OnPoint backscatter detector. The volume was collected at 3 kV, with 10.8 nm pixels x and y; 70 nm Z steps and 70% local gas injection. The raster size was 25k x 12k and the volume was aligned using cross correlation and visualized using IMOD.
DOI: 10.6075/j0df6rfv
title: CIL: 54844, Conchiformibius steedae, bacteria. In Cell Image Library

description: Leica TCS SP8 X; 63X Plan-Apochromat glycerine objective with a NA of 1.30 and a refraction index of 1.46.
description: Imaging mode: confocal microscopy
Visualization methods: fluorescent d amino acids
description: Screnshot showing the position of a synthesized septum within the C. steedae filament.
DOI: 10.6075/j0cj8dpb
title: CIL: 54848, Danio rerio, Whole larva. In Cell Image Library

description: Larvae preparation for GFP+ CLEM (eLife: Workflow #2). To facilitate the 3D correlation between different imaging modalities when using any GFP+ transgenic line, we added DRAQ5, a nuclear DNA binding fluorescent dye. Briefly, the 5 dpf transgenic zebrafish larvae were fixed with 0.5% glutaraldehyde and 2% paraformaldehyde in 0.15M cacodylate buffer (CB, pH 7.4) for 2.5 hours and 100 m thick sagittal sections were collected and incubated in DRAQ5 (1:1000, Cell Signaling Technology) on ice for an hour. Confocal images of GFP and DRAQ5 signals were collected on a Leica SPE II confocal microscope with a 20X oil-immersion objective lens using 488 nm and 633 nm excitation. Following, the samples were preincubated in 2.5 mM DAB solution (25.24 mM stock in 0.1 M HCl) in 0.15 M CB for 30 min on ice. Next, the photo-oxidation of DAB by DRAQ5 was done in 2.5 mM DAB in 0.15 M CB using a solar simulator (Spectra-Physics 92191–1000 solar simulator with 1600 W mercury arc lamp and two Spectra-Physics SP66239–3767 dichroic mirrors to remove infrared and ultraviolet wavelengths), while bubbling oxygen in the solution. The light was filtered through a 10 cm square bandpass filters (Chroma Technology Corp.) for illumination at 615 nm (40 nm band pass). The reaction was monitored every 20 minutes and stopped when the desired darkening in the nuclei was achieved. Larvae were then washed 5 times with 0.15 M CB and incubated in 2% OsO4/1.5% potassium ferrocyanide in 0.15 M CB containing 2 mM CaCl2 to get an EM visible stain. The larvae were left for 30 min on ice and then 30 min at room temperature (RT). After thorough washing in double distilled water (ddH2O), larvae were placed into 0.05% thiocarbohydrazide for 30 min. Larvae were again washed and then stained with 2% aqueous OsO4 for 30 min. Larvae were washed and then placed into 2% aqueous uranyl acetate overnight at 4°C. Larvae were washed with ddH2O at RT and then stained with 0.05% en-bloc lead aspartate for 30 min at 60°C. Larvae were washed with ddH2O and then dehydrated on ice in 50%, 70%, 90%, 100%, 100% ethanol solutions for 10 min at each step. Larvae were then washed twice with dry acetone and placed into 50:50 Durcupan ACM:acetone overnight. Larvae were transferred to 100% Durcupan resin overnight. Larvae were then flat embedded between glass slides coated with mould-release compound and left in an oven at 60°C for 72 h. The larva block was imaged with a Merlin scanning electron microscope equipped with a 3View2XP and OnPoint backscatter detector. The volume was collected at 3 kV, with 10.8 nm pixels x and y ; 70 nm Z steps and 70% local gas injection. The raster size was 25k x 12k and the volume was aligned using cross correlation and visualized using IMOD.
description: Sagittal sections of 5 days post-fertilization dbh:gfp+ zebrafish larva in the region of the anterior kidney (eLife Table 1: dbh:GFP 5 dpf).
description: Imaging mode: SBEM
DOI: 10.6075/j0wh2q5c
title: CIL: 54878. In Cell Image Library

description: The adoption of cell-based therapies into the clinic will require tremendous large-scale expansion to satisfy future demand, and bioreactor-microcarrier cultures are best suited to meet this challenge. A robust optical imaging and image-analysis assay to non-destructively quantify cell number and cell volume was developed using fluorescence and elastic scattering contrast. This assay was successfully applied to monitor cellular growth of induced pluripotent derived mesenchymal stem cells (iH-MSCs) attached to spherical hydrogel microcarriers over time. Elastic scattering and fluorescence lightsheet microscopy were used to quantify cell volume and cell number at varying spatial scales. The fluorescence-based assay is used as ground truth data to correlate the elastic scattering-based assay data.

Fig 2d Fixed passage 7 day 3 ih-MSC infiltrating the center of a microcarrier.
description: Imaging mode: Zeiss Z.1 Lightsheet microscope (fluorescence and scattering)
Visualization methods: FIJI/ImageJ
description: ih-MSCs were cultured in a rotating wall vessel (RWV) bioreactor (RCCS-8DQ bioreactor (Synthecon, Houston, TX) fitted with 10 mL high aspect ratio vessels on custom-fabricated 120 ± 6.2 μm diameter gelMA microcarriers. For this purpose, approximately 110,000 gelMA microcarriers with a combined growth area of 50 cm2 and 5×104 cells (1000 cells/cm2) were incubated in 10 mL of CCM in the RWV bioreactor at 24 revolutions per minute. Half of the media was replaced with fresh CCM every 2 days. iH-MSCs fixed with 4% paraformaldehyde and fluorescently labeled with CellTracker Green (green), DRAQ-5 (blue), and DiI (gold) in the cytoplasm, nuclei, and plasma membrane, respectively. Label-free elastic scattering (white) and trasmitted light (grey) are also used to visualize the sample.

Passage 7 Day 3 single cell labeled with DiI in the plasma membrane.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
DOI: 10.6075/j0j67h44
title: CIL: 54874. In Cell Image Library

description: ih-MSCs were cultured in a rotating wall vessel (RWV) bioreactor (RCCS-8DQ bioreactor (Synthecon, Houston, TX) fitted with 10 mL high aspect ratio vessels on custom-fabricated 120 ± 6.2 μm diameter gelMA microcarriers. For this purpose, approximately 110,000 gelMA microcarriers with a combined growth area of 50 cm2 and 5×104 cells (1000 cells/cm2) were incubated in 10 mL of CCM in the RWV bioreactor at 24 revolutions per minute. Half of the media was replaced with fresh CCM every 2 days. iH-MSCs fixed with 4% paraformaldehyde and fluorescently labeled with CellTracker Green (green), DRAQ-5 (blue), and DiI (gold) in the cytoplasm, nuclei, and plasma membrane, respectively. Label-free elastic scattering (white) and trasmitted light (grey) are also used to visualize the sample.

Passage 4 Day 3 single cell labeled with CelllTracker Green in the cytoplasm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
description: Imaging mode: Zeiss Z.1 Lightsheet microscope (fluorescence and scattering)
Visualization methods: FIJI/ImageJ
description: The adoption of cell-based therapies into the clinic will require tremendous large-scale expansion to satisfy future demand, and bioreactor-microcarrier cultures are best suited to meet this challenge. A robust optical imaging and image-analysis assay to non-destructively quantify cell number and cell volume was developed using fluorescence and elastic scattering contrast. This assay was successfully applied to monitor cellular growth of induced pluripotent derived mesenchymal stem cells (iH-MSCs) attached to spherical hydrogel microcarriers over time. Elastic scattering and fluorescence lightsheet microscopy were used to quantify cell volume and cell number at varying spatial scales. The fluorescence-based assay is used as ground truth data to correlate the elastic scattering-based assay data.

Fig 1a Fixed passage 4 day 3 ih-MSC on a gelMA microcarrier.
DOI: 10.6075/j0x63mqw
title: CIL: 54510. In Cell Image Library

description: Atypical family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j0f18zbx
title: CIL: 53420, Pseudo-nitzchia arctica, Plankton. In Cell Image Library

description: 128x128 segmented image from volumetric hologram
description: Imaging mode: Holography
Visualization methods: Amplitude Mode
description: Choanoflagellate
DOI: 10.6075/j0sn08mh
title: CIL: 53358, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: 9.4 degrees ℃
description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 9.4 degrees Celcius
DOI: 10.6075/j01j99f7
title: CIL: 53495, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: AGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0d50mh2
title: CIL: 52378, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=2, z=17 from BL024199_Myc_Terc
DOI: 10.6075/j09k49t3
title: CIL: 53112, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Image 2, z=16 from SC_030
description: One z layer of a z-stack at the given image
DOI: 10.6075/j0mp52vv
title: CIL: 52769, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=7, y=2, z=9 from PS11_10021_2B_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0c82920
title: CIL: 54195, Homo sapiens, HeLa. In Cell Image Library

description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
DOI: 10.6075/j0gm871c
title: CIL: 54079. In Cell Image Library

description: Visualization methods: confocal microscopy
description: TK family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
DOI: 10.6075/j08w3ctb
title: CIL: 52463, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=1, y=5, z=18 from BL32077_Myc_Terc
description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j09886jp
title: CIL: 52582. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=1, y=6, z=11 from PS09_20676_2B_Myc_Terc
DOI: 10.6075/j0mk6cms
title: CIL: 54047, Homo sapiens, HeLa. In Cell Image Library

description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: Visualization methods: confocal microscopy
description: STE family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0183621
title: CIL: 52882, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Tile x=4, y=5, z=17 from PS11_167511L_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns