cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30497669.v1
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.
DOI: 10.6075/j0n58m67
title: CIL: 54692, Bacteria E coli, MC1061. In Cell Image Library

description: sfGFP with TIR-EVLO site.
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: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
DOI: 10.6075/j0wh2ppp
title: CIL: 54475, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
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: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled by Bielschowsky's silver stain.
DOI: 10.6075/j0n016c4
title: CIL: 54725. 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. Stereo viewing and computer assisted serial reconstruction techniques were employed to visualize three-dimensional relationships among cytoplasmic components of cortical neurons.
description: Item type: EM tomogram
Imaging mode: SEM survey
description: 2D survey of cerebral cortex.
DOI: 10.6075/j0zk5gd2
title: CIL: 54499, 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/j0gt5n2q
title: CIL: 54825, Alysiella filiformis, bacteria. In Cell Image Library

description: A. filiformis filament after incubation with HADA 30 min, TADA for 15 min, BADA 15 minutes.
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
DOI: 10.6075/j0k9378f
title: CIL: 54593, Mus musculus, Fetal Liver Macrophage. In Cell Image Library

description: Constitutive macropinocytosis
description: Processed data
description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
DOI: 10.25919/ffjf-0r37
title: Bathymetry surveys for Fitzroy Estuary QLD and Cassady and Palm Cks (Hinchinbrook, QLD) 2024-25: CSIRO Tidal Inundation Project

description: This dataset compiles field survey information derived from multibeam sonar data captured for the CSIRO Tidal Inundation Project, 2024-25. The dataset consists of Cloud Optimised GeoTiff and XYZ files at varying spatial resolutions for the bathymetric surveys carried out during this project. Survey data is presented at spatial resolutions of 2 metres, 1 metre and, for the Hinchinbrook sites, 50 centimetre spacing.
DOI: 10.6075/j0w095s9
title: CIL: 54824, Alysiella filiformis, bacteria. In Cell Image Library

description: Nikon Eclipse NI-U microscope equipped with a MFCool camera (Jenoptik).
description: Imaging mode: fluorescence microscopy
Visualization methods: fluorescent d amino acids
description: A. filiformis filaments after incubation with TADA for 15 minutes.
DOI: 10.6075/j0pn95jv
title: CIL: 54768, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: GATA4
DOI: 10.6075/j0kp821x
title: CIL: 54799, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Confocal fluorescent imaging
description: DAPI staining
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6075/j0fb52k8
title: CIL: 54434, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: AT8 IHC using HRP/DAB
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for phosphorylated tau (AT8).
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/j02f7n93
title: CIL: 54651, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
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: Confocal image of the CNS of a control D. melanogaster in the third instar larval stage, 0uM 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 glial and astrocytes after disruption of cortex glial morphology. In a control animal, there is a separation between the two glial subtypes.
DOI: 10.6075/j0cc10kn
title: CIL: 54756, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Oct4 staining
DOI: 10.6075/j0xk8f6s
title: CIL: 54428, Homo sapiens. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for amyloid-beta (4G8).
description: Imaging mode: bright-field microscopy
Visualization methods: 4G8 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/j0dn44x0
title: CIL: 54684. In Cell Image Library

description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after αSNAP KD, 32uM 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 astrocytes after disruption of cortex glial morphology. After knockdown of αSNAP, a protein part of the vesicual transport pathway, 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/j03r0sk3
title: CIL: 54441, Homo sapiens, astrocyte. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for glial fibrillary acidic protein (GFAP), a protein commonly used to identify astrocytes.
description: Imaging mode: bright-field microscopy
Visualization methods: GFAP 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/j0gt5mt5
title: CIL: 54423, Homo sapiens. In Cell Image Library

description: Imaging mode: bright-field microscopy
Visualization methods: 4G8 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.
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic donor labeled for amyloid-beta (4G8).
DOI: 10.6075/j0w095hq
title: CIL: 52798, 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=1, y=1, 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
DOI: 10.6075/j0td9x2h
title: CIL: 53787. In Cell Image Library

description: CMGC 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/j069735j
title: CIL: 53217, Entire Organism, Overall development. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: Video of African clawed frog embryonic development. Each video is labeled with the temperature (Celcius) at which it was captured and the name of the Time Course (##TC).
DOI: 10.6075/j0gh9hn3
title: CIL: 53718. In Cell Image Library

description: CMGC 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/j0h70g1r
title: CIL: 54885. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: uranium compound
description: Cut the yellow leaves and green leaves in 3 stages into 2mm × 2mm size, fixed with 2.5 % glutaraldehyde solution, and rinsed 3 times with 0.1 M phosphate buffer (pH 7.0) 3 times for 15 min each time, fixed with 1% osmic acid for 4 h, and rinsed with phosphate buffer for 3 times. Conventional gradient ethanol series dehydration is treated with the mixture of embedding agent and acetone with a volume ratio of 1/1 and 3/1. The pure 812 resin was embedded, polymerized at 70 ℃ for 8 hours, sliced with an ultrathin slicer at 60-80 nm, and stained with uranyl acetate and lead citrate. The images were collected to analyze and compare the internal changes of leaves at different stages and positions.

Staining: chloroplast in yellow and green parts of leaves.
description: With the maturity of the leaves, the main changes of the green leaves are the increase in the number of chloroplasts, and the shape of the chloroplasts gradually takes on a spindle shape, and the color shows from light green to dark green. The same is true for the changes of the yellow leaf parts. Its chloroplast number gradually increases and its internal structure gradually completes, including the increase of grana stacking and the decrease of osmophilic granules. The appearance color of the chloroplast was from bright yellow to dark yellow. Secondly, at the same stage, the chloroplast morphology of the green leaves was normally spindle-shaped, with a large number of grana stacked into grana lamellae, neatly arranged, and a large number of starch granules (Fig. 1A-D, I-L, Q-T). The chloroplasts in the yellow leaves were nearly round, with incomplete structural development, such as no obvious stacking of grana, and a large number of osmophilic granules aggregated (Fig. 1 E-H, M-P, U-X).
DOI: 10.6075/j09p31vw
title: CIL: 54861. In Cell Image Library

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
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: osmium tetroxide
DOI: 10.6075/j0ff3sjs
title: CIL: 54858. In Cell Image Library

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
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: osmium tetroxide
DOI: 10.6075/j0416x82
title: CIL: 54866. 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 1h Fixed passage 7 day 7 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 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
DOI: 10.6075/j07s7p0g
title: CIL: 54875. 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 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 1i Fixed Passage 4 day 3 ih-MSC on a gelMA microcarrier.