cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j05t3kpd
title: CIL: 54871. In Cell Image Library

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 4 Day 7 cells labeled with CelllTracker Green in the cytoplasm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
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 1b Fixed passage 4 day 7 ih-MSC on a gelMA microcarrier.
DOI: 10.6075/j09k4bfk
title: CIL: 54857. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: osmium tetroxide
description: Lipid droplet interaction with mitochondria and endoplasmic reticulum in inflammatory neutrophils. The sequence of images in different magnifications shows a transversal sections of the neutrophils. Below plasma membrane is possible to identify the types of contacts between lipid droplet, mitochondria, and endoplasmic reticulum. Neutrophil were observed in inflammatory exudate obtained after 6 hours of Leishmania infantum (MCAN/BR/89/BA262)injection into the peritoneal cavity . Cells were fixed using karnovsky reagent, post-fixed with osmium tetroxide, dehydrated in ethanol and embedded in epoxy resin. Thin sections were viewed on a Zeiss 109 transmission electron microscope. Magnifications 120000, 80000, 50000,10000 and 5000.
description: * Karnovsky fixed tissue
* Osmium tetroxide fixed tissue
* Cells in epoxy resin embedment
DOI: 10.6075/j0k35tvs
title: CIL: 54852. In Cell Image Library

description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays the PHF array.
description: Imaging mode: Electronic tomography
DOI: 10.6075/j0n016qm
title: CIL: 54872. 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 1j Fixed Passage 4 day 7 ih-MSC on a gelMA 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 4 Day 7 cells labeled with DRAQ-5 in the nuclei.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
DOI: 10.6075/j0rr1zd6
title: CIL: 54879. 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 7 Day 3 single cell labeled with DRAQ-5 in the nucleus.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
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 2b 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
DOI: 10.6075/j0513zdf
title: CIL: 54876. In Cell Image Library

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 1e Fixed passage 4 day 3 ih-MSC on a gelMA microcarrier.
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 imaged with elastic scattering contrast and illuminated with 638 nm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
DOI: 10.6075/j0z89cmx
title: CIL: 54845, Danio rerio, Whole larva. In Cell Image Library

description: Transverse sections of 5 days post-fertilization wild-type zebrafish larva in the region of the anterior kidney.
description: Brief description of sample preparation and SBEM imaging

5 d.p.f. zebrafish larva was prepared for SBEM. Larva was 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, larva was treated for 15 minutes with 20 mM glycine in 0.15M CB, on ice to quench the unreacted glutaraldehyde. Then, larva was 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 larva was left for 30 min on ice and then 30 min at room temperature (RT). After thorough washing in double distilled water (ddH2O), larva was placed into 0.05% thiocarbohydrazide for 30 min. Larva was again washed and then stained with 2% aqueous OsO4 for 30 min. Larva was washed and then placed into 2% aqueous uranyl acetate overnight at 4°C. Larva was washed with ddH2O at RT and then stained with 0.05% en bloc lead aspartate for 30 min at 60°C. Larva was washed with ddH2O and then dehydrated on ice in 50%, 70%, 90%, 100%, 100% ethanol solutions for 10 min at each step. Larva was then washed twice with dry acetone and placed into 50:50 Durcupan ACM:acetone overnight. Larva was transferred to 100% Durcupan resin overnight. Larva was 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 a Zeiss Gemini scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 4.0 kV accelerating voltage with a 30 μm condenser aperture and 0.5 μsec dwell time; Z step size was 70 nm; pixel size was 9.5 nm; raster size was 25k x 12k, variable pressure under nitrogen. The volume was aligned using cross correlation, segmented, and visualized using IMOD.
description: Imaging mode: SBEM
DOI: 10.6075/j00865h8
title: CIL: 54880. In Cell Image Library

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 imaged with elastic scattering contrast and illuminated with 638 nm.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
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 2e Fixed passage 7 day 3 ih-MSC infiltrating the center of a microcarrier.
DOI: 10.6075/j0bk1ckz
title: CIL: 54873. 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 cells 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.

Passage 7 Day 7 cells labeled with CelllTracker Green in the cytoplasm.
DOI: 10.6075/j0th8mxn
title: CIL: 54854. In Cell Image Library

description: Imaging mode: Electronic tomography
description: We examined the structural organization of cytoskeletal components and membrane systems in neurons of well preserved biopsy material from Alzheimer’s disease (AD). Information was obtained from thin sectioned material using conventional electron microscopy and from thick sections with the high voltage electron microscope.
description: This image displays the PHF array.
DOI: 10.6075/j06t0mv7
title: CIL: 54842, Conchiformibius steedae, bacteria. In Cell Image Library

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.
description: Leica TCS SP8 X; 63X Plan-Apochromat glycerine objective with a NA of 1.30 and a refraction index of 1.46.
DOI: 10.6075/j0nv9jg8
title: CIL: 54889, Saccharomyces cerevisiae, Single cell. In Cell Image Library

description: Miller chromatin spread. For yeast technique see: Osheim YN, French SL, Sikes ML, Beyer AL. Electron microscope visualization of RNA transcription and processing in Saccharomyces cerevisiae by Miller chromatin spreading. Methods Mol Biol. 2009;464:55-69. doi: 10.1007/978-1-60327-461-6_4. PMID: 18951179.
description: Part of a collage of images of a single nucleolus from yeast strain NOY1051 which has a fixed rDNA array size of 143 repeats. In total 71 of 120 35S ribosomal RNA genes visualized in the Miller chromatin spread from this cell are transcriptionally active. An overview of this nucleolus photographed at low magnification is published in French et al. (2008) Mol Cell Biol. 28:4576-87, Fig. 3A. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447126/figure/f3/
description: Preparation: Image was captured at a magnification of 6600X on electron microscope film, then enlarged an additional 3.25X when printed onto photographic paper and scanned at 600 dpi.
Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Uranyl acetate; phosphotungstic acid
DOI: 10.6075/j0vh5p10
title: CIL: 54864. 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 7 Day 7 cells 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 1d Fixed passage 7 day 7 ih-MSC on a gelMA microcarrier.
DOI: 10.6075/j0sq90kv
title: CIL: 54846, Danio rerio, Whole larva. In Cell Image Library

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.
description: Sagittal sections of 5 days post-fertilization drl:APEX2-mCherry+ zebrafish larva in the region of the anterior kidney (eLife Table 1: APEX2 #2 5 dpf).
description: Imaging mode: SBEM