cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0kp81tt
title: CIL: 53631, Homo sapiens, HeLa. 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: 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/j0w66k9x
title: CIL: 52561, 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=4, z=11 from BL32080_Myc_Terc
DOI: 10.6075/j0gm872t
title: CIL: 54288, 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: CAMK 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/j08c9w37
title: CIL: 54784, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: TUBB3 staining
description: Epifluorescent imaging
DOI: 10.6075/j01n810r
title: CIL: 54625, Mus musculus, oocyte. In Cell Image Library

description: FIG.2E Changes in ER cluster morphology require gamete fusion.
description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
DOI: 10.6075/j070816r
title: CIL: 54496, Homo sapiens, astrocyte. In Cell Image Library

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
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.
DOI: 10.6075/j0q81cz6
title: CIL: 54645. In Cell Image Library

description: Item type: Serial section
Imaging mode: transmission electron microscopy (TEM)
description: Degenerating neuron with PHF and lipofuscin. This image exhibits mild degeneration.
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.
DOI: 10.6075/j0j38sdc
title: CIL: 54749, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: DAPI staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
DOI: 10.6075/j07p8z3g
title: CIL: 54480, 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/j0wh2pvx
title: CIL: 54723. 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: Degraded neuron with lipofuscin.
description: Item type: Serial section
Imaging mode: transmission electron microscopy (TEM)
DOI: 10.6075/j0cr5t6z
title: CIL: 54663, 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 D. melanogaster in the third instar larval stage after Spz3 KD, 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 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.
DOI: 10.6075/j00v8cn5
title: CIL: 54601, Mus musculus, Fetal Liver Macrophage. In Cell Image Library

description: Membrane Structure Comparison
description: Processed data
description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
DOI: 10.6075/j0m908h5
title: CIL: 54671, Drosophila melanogaster, astrocytes (red). In Cell Image Library

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 D. melanogaster in the third instar larval stage after Spz3 KD, 72uM 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: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
DOI: 10.6075/j0qc03bg
title: CIL: 54833, Simonsiella muelleri, 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: S. muelleri filaments after incubation with TADA for 30 minutes.
DOI: 10.6075/j0gq6xmj
title: CIL: 54639, Mus musculus, oocyte. In Cell Image Library

description: FIG. 4H 4H' Changes in cortical ER clusters at the site of sperm binding and incorporation.
description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
DOI: 10.6075/j0pr7vt0
title: CIL: 54740, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: confocal laser scanning microscopy
Visualization methods: bright field imaging
description: Live cell imaging.
description: Cells imaged with bright field.
DOI: 10.6075/j0251j2p
title: CIL: 54714, Bacteria E coli, MC1061. In Cell Image Library

description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
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: mNeonGreen with TIR-STD site, scale bar 4 um.
DOI: 10.6075/j0k64hz2
title: CIL: 54711, Bacteria E coli, MC1061. In Cell Image Library

description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
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: mNeonGreen with TIR-EVLO site.
DOI: 10.6075/j06d5sv2
title: CIL: 54616, Phakopsora Pachyrhizi. In Cell Image Library

description: The sequenced reference P. pachyrhizi strain K8108 is a single urediniosoral isolate from P. pachyrhizi-infected soybean leaves collected in 2015 in Uruguay (Colonia region). Genome sequence of this isolate is available at 
https://mycocosm.jgi.doe.gov/PhapaK8108/PhapaK8108.home.html.
description: Imaging mode: time lapse microscopy
description: Snaphot images at 9 time points from 90 to 210 min after mixing with different compounds. Organised by time point and compound.
DOI: 10.6075/j0gf0tc4
title: CIL: 54701, Bacteria E coli, MC1061. In Cell Image Library

description: mPAmCherry post-activation with TIR-EVOL site.
description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
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)
DOI: 10.6075/j0x066w7
title: CIL: 54815. 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: Item type: EM tomogram
Imaging mode: Serial-section SEM
description: This image is a survey volume from cerebral cortex to identify cells exhibiting hallmarks for AD degeneration.
DOI: 10.6075/j0qz29tv
title: CIL: 54703, Bacteria E coli, MC1061. In Cell Image Library

description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
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: mPAmCherry pre-activation with TIR-EVOL site.
DOI: 10.6075/j05x28sp
title: CIL: 54712, Bacteria E coli, MC1061. In Cell Image Library

description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
description: mNeonGreen with TIR-EVLO site, scale bar 4 um.
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)
DOI: 10.6075/j0b857sd
title: CIL: 54443, 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: 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: 4G8 IHC using HRP/DAB
DOI: 10.6084/m9.figshare.30435706
title: Undergraduate student academic performance

description: Research conducted to predict academic performance of first-year undergraduate students at one regional, Australian university. One of the measures used in the model was a post-entry language assessment (PELA). GPA data was collected after two semesters of study.
DOI: 10.6084/m9.figshare.30435706.v1
title: Undergraduate student academic performance

description: Research conducted to predict academic performance of first-year undergraduate students at one regional, Australian university. One of the measures used in the model was a post-entry language assessment (PELA). GPA data was collected after two semesters of study.
DOI: 10.6075/j08w3d6p
title: CIL: 54689, 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 D. melanogaster in the third instar larval stage after Spz3 KD, 16uM 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.
DOI: 10.6075/j0z03811
title: CIL: 54807, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: iRFP720 imaging of spheroids.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: Spheroid imaging
DOI: 10.6075/j0dz086t
title: CIL: 54809. In Cell Image Library

description: This image displays degenerating neuron with the cristae junction.
description: Item type: EM tomogram
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.
DOI: 10.6075/j0ft8kwg
title: CIL: 54618, Phakopsora Pachyrhizi. In Cell Image Library

description: The sequenced reference P. pachyrhizi strain K8108 is a single urediniosoral isolate from P. pachyrhizi-infected soybean leaves collected in 2015 in Uruguay (Colonia region). Genome sequence of this isolate is available at 
https://mycocosm.jgi.doe.gov/PhapaK8108/PhapaK8108.home.html.
description: Imaging mode: time lapse microscopy
description: Time-lapse videos of germination in presence of the different compounds.
DOI: 10.6075/j07p8z78
title: CIL: 54728. 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: Item type: EM tomogram
Imaging mode: Electronic tomography
DOI: 10.6075/j0qc0391
title: CIL: 54614. 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 Merlin 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 1.0 μsec dwell time; Z step size was 40 nm; pixel size was 4.11 nm; raster size was 14k x 14k; Z dimension was 1559 sections, and local gas injection was set to 85%. 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/j0086567
title: CIL: 54730. In Cell Image Library

description: This image displays the PHF array.
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: Item type: EM tomogram
Imaging mode: Electronic tomography
DOI: 10.6075/j0kh0n6f
title: CIL: 54648, 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 control D. melanogaster in the third instar larval stage, 16uM 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.
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/j0zc82q6
title: CIL: 54707, 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: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
description: mEos3.2 with TIR-EVLO site.