cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0x92bhj
title: CIL: 54865. 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 DRAQ-5 in the nuclei.

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 1l Fixed Passage 7 day 7 ih-MSC on a gelMA microcarrier.
DOI: 10.6075/j0sn0953
title: CIL: 54883. 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 aggregate labeled with DRAQ-5 in the nuclei.

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.

Fig3c Fixed passage 4 day 7 ih-MSc microcarrier aggreagate.
DOI: 10.6075/j0222tz0
title: CIL: 54869. 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 1k Fixed Passage 7 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 7 Day 3 cells labeled with DRAQ-5 in the nuclei.

Staining: Cytoplasm (green); plasma membrane (gold); nucleus (blue); whole cell (elastic scattering white)
DOI: 10.6075/j0416xdv
title: CIL:57190, Homo sapiens. In Cell Image Library

description: Imaging mode: scanning electron microscopy (SEM)
description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPES was added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
DOI: 10.6075/j04t6jkg
title: CIL: 54892, Saccharomyces cerevisiae, Single cell. In Cell Image Library

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
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/
DOI: 10.6075/j0db822c
title: CIL: 54890, Saccharomyces cerevisiae, Single cell. In Cell Image Library

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: 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: 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/j0h995jv
title: CIL:57188, Homo sapiens. In Cell Image Library

description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPESwas added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
description: Imaging mode: scanning electron microscopy (SEM)
DOI: 10.6075/j03f4pd1
title: CIL: 54489, Homo sapiens. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for phosphorylated tau (AT8).
description: Imaging mode: bright-field microscopy
Visualization methods: AT8 IHC using HRP/DAB
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
DOI: 10.6075/j0br8rvg
title: CIL: 54455, Homo sapiens. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled by Bielschowsky's silver stain.
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
DOI: 10.6075/j08915rb
title: CIL: 54819, Alysiella filiformis, bacteria. In Cell Image Library

description: A. filiformis filament
description: Nikon Eclipse NI-U microscope equipped with a MFCool camera (Jenoptik).
description: Imaging mode: phase contrast microscopy
DOI: 10.6075/j02z156v
title: CIL: 54461, Homo sapiens, astrocyte. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for glial fibrillary acidic protein (GFAP), a protein commonly used to identify astrocytes.
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: Imaging mode: bright-field microscopy
Visualization methods: GFAP IHC using HRP/DAB
DOI: 10.6075/j0416wtt
title: CIL: 54487, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: hematoxylin and eosin
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for hematoxylin and eosin.
description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
DOI: 10.6075/j0vt1rzh
title: CIL: 54669, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after Spz3 KD, 38uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocyte after disruption of cortex glial morphology. After knockdown of Spz3, a secreted neurotrophin, we observed aberrant infiltration by astrocytes into the cortex.
description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
DOI: 10.6075/j0gx4bd4
title: CIL: 54794, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: Confocal fluorescent imaging
description: SOX17 staining
DOI: 10.6075/j01c1wrj
title: CIL: 54690, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after Spz3 KD, 12uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocyte after disruption of cortex glial morphology. After knockdown of Spz3, a secreted neurotrophin, we observed aberrant infiltration by astrocytes into the cortex.
description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
DOI: 10.6075/j0pz58qx
title: CIL: 54708, Bacteria E coli, MC1061. In Cell Image Library

description: Imaging mode: EPI on a Nikon TiE2 Hamamatsu ORCA Flash 4.0 sCMOS Camera and Nikon SR Apo TIRF 100x objective lens (NA 1.49)
description: mEos3.2 with TIR-EVLO site, scale bar 4 um.
description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
DOI: 10.6075/j07d2tz0
title: CIL: 54608. In Cell Image Library

description: Drosophila antennae were prepared as described in Tsang et al. After cryofixation by high-pressure freezing and freeze-substitution in a cocktail containing uranyl acetate and glutaraldehyde, cryofixed antennae were rehydrated gradually at ice temperature. Rehydrated samples were then subjected to DAB labeling reaction and stained using a high-contrast en bloc staining protocol. Next, the samples were dehydrated for resin infiltration and embedded in Durcupan epoxy, followed by imaging with X-ray microscopy and then serial block-face scanning electron microscopy.

The antenna was imaged using a Zeiss Gemini scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 2.5 kV accelerating voltage with a 30 μm condenser aperture and 2.5 μsec dwell time; Z step size was 50 nm; pixel size was 3.85 nm; raster size was 20k x 13.75k; Z dimension was 999 sections, and variable pressure under nitrogen. Volume was aligned using cross correlation, segmented, and visualized using IMOD.
description: Item type: recorded image
Imaging mode: serial block face SEM (SBFSEM)
description: The biophysical properties of sensory neurons are influenced by their morphometric and morphological features, whose precise measurements require high-quality volume electron microscopy (EM). However, systematic surveys of these nanoscale characteristics for identified neurons are scarce. Taking advantage of the CryoChem method, which permits high-quality ultrastructural preservation of cryofixed and genetically labeled samples for volume EM, we acquired serial block-face scanning electron microscopy (SBEM) images of antennal tissues in which select ORNs expressed the APEX2 EM marker. These SEBEM datasets allow a systematic morphometric and morphological analysis of identified olfactory receptor neurons in Drosophila melanogaster.
DOI: 10.6075/j06t0mg9
title: CIL: 54737, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Live cell fluorescent imaging.
description: Cells stained with viability indicator dye fluorescein diacetate.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6084/m9.figshare.30497669
title: Data and codes for "Air Pollution Control and Green Transformation: Economic Impacts of China’s Ten Measures for Air Policy"

description: Attached are data and codes for manuscript "Air Pollution Control and Green Transformation: Economic Impacts of China’s Ten Measures for Air Policy". All for STATA software.