cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0cv4hhx
title: CIL: 54482, 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 hematoxylin and eosin.
description: Imaging mode: bright-field microscopy
Visualization methods: 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/j0k0744t
title: CIL: 54739, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: iRFP720 expressing cells stained with viability indicator dye fluorescein diacetate (merged image).
description: Live cell fluorescent imaging.
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6075/j0v69jgk
title: CIL: 54798, 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: PDX1 staining
DOI: 10.6075/j0g44q0c
title: CIL: 54476, Homo sapiens. 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/j03x86bp
title: CIL: 54479, Homo sapiens. In Cell Image Library

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.
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for phosphorylated tau (AT8).
DOI: 10.6075/j09023m9
title: CIL: 54658, 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, 36uM 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/j0vh5nqj
title: CIL: 54731. In Cell Image Library

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.
description: This image displays the PHF array.
DOI: 10.6075/j08c9vt7
title: CIL: 52764, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=7, y=2, z=4 from PS11_10021_2B_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j08915dv
title: CIL: 52589. In Cell Image Library

description: Tile x=1, y=6, z=18 from PS09_20676_2B_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
DOI: 10.6075/j0qn66c6
title: CIL: 53378, Homo sapiens, HeLa. In Cell Image Library

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
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/j05t3k0f
title: CIL: 52517, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: One z layer of a z-stack at the given tile position
description: Tile x=5, y=4, z=9 from BL32077_Myc_Terc
DOI: 10.6075/j0474b2n
title: Patient and section data accompanying Pediatric Inflammatory Bowel Disease dataset. In Cell Image Library

description: The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist.
DOI: 10.6075/j0w37vz3
title: CIL: 54816, Homo sapiens Linnaeus, 1758, epithelial cell. In Cell Image Library

description: We use in-situ harvest method and trypsin/Wright stain procedure to prepare G-banding. Briefly, the amniotic cells were cultured in BIO-AMF medium (Biological industrial, Beit-Haemek, Israel) for 6 to 8 days.Treating cells with colcemid (NY, USA, Gibco) for 30 min to arrest cells at metaphase. Swell cells with hypotonic solution and fix with methanol/acetic acid mixture. Fixed cells were treated with tryspin then stained with Wright stain solution (MO, Sigma-Aldrich). The karyotype was interpreted according to The International System for Human Cytogenomic Nomenclature (ISCN). 

See also: M. J. Barch, T. Kuntsen and J. L. Spurbeck, The AGT Cytogenetics Laboratory Manual, Lippincott-Raven (1997). Yunis J. High resolution of human chromosome. Science 1976: 191:1268-1270. J. McGowan-Jordan, A.
Sim+A13ons and M. Schmid. An International System for Human Cytogenetic Nomenclature. KARGER (2016).
description: Imaging mode: recorded image
Visualization methods: trypsin/Wright stain
description: Using a camera mounted above the microscope, experts adjust the lens and angle to capture the stain and transfer the image to a computer for processing.
DOI: 10.6075/j07m06r5
title: CIL:41456, diatom. In Cell Image Library

description: Relation to intact cell: tissue in styrax resin
Item type: recorded image
Imaging mode: interference contrast
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
description: Fossil of an extinct diatom from Tertiary deposits in Dunkirk, Maryland. The diatom is approximately 80 microns in diameter. The image is of a diatom valve (two valves and a girdle band compose a diatom frustule or shell). The image was captured using Zeiss Jamin-Lebedeff Interference Contrast with a 40x objective. The image is of a diatom valve. Digital image stacking was also used to provide a greater depth of focus than would be possible with a single exposure. It is a stack of three separate exposures processed through Helicon Focus, which extracts pixels in focus in each image and then outputs a composite.
 Third Prize, 2008 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0q24022
title: CIL: 54675, 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 αSNAP KD, 82uM 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/j0j67gkj
title: CIL: 54430, Homo sapiens. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic 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/j0b56jm7
title: CIL: 54802, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Spheroid imaging
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: Brightfield and DAPI imaging merged.
DOI: 10.6075/j0mw2h0z
title: CIL: 54755, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: TRA1-81 staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
DOI: 10.6075/j0tx3f4h
title: CIL: 54490, Homo sapiens. 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: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled by Bielschowsky's silver stain.
description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
DOI: 10.6075/j0ns0tr2
title: CIL: 54746, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Nanog staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
DOI: 10.6075/j02b8xwc
title: CIL: 54682, 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: 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 αSNAP KD, 8uM 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.
DOI: 10.6075/j0td9x7r
title: CIL: 54769, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: DAPI staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
DOI: 10.6075/j0j67gs7
title: CIL: 54721. 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: Serial-section
Imaging mode: Serial-section SEM
description: This image is a 2D survey mosaic of cerebral cortex.
DOI: 10.6075/j0028r7d
title: CIL: 54464, Homo sapiens. 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: 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
DOI: 10.6075/j0s1826g
title: CIL: 54469, 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 Alzheimer's disease 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/j0np249p
title: CIL: 54782, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Brachyury staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
DOI: 10.6075/j0db81qg
title: CIL: 54748, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Nanog staining
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
DOI: 10.6075/j05x28nw
title: CIL: 54459, Homo sapiens. 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: AT8 IHC using HRP/DAB
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for phosphorylated tau (AT8).
DOI: 10.6075/j03r0srb
title: CIL: 54795, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Confocal fluorescent imaging
description: FOXA2 staining
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
DOI: 10.6075/j0x63mt7
title: CIL: 54780, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Epifluorescent imaging
description: GATA4
DOI: 10.6075/j0cv4hdk
title: CIL: 54451, Homo sapiens, astrocyte. In Cell Image Library

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.
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.
DOI: 10.6075/j00z734s
title: CIL: 54786, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: DAPI staining
description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
DOI: 10.6075/j0tq61d6
title: CIL: 54709, 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-STD site.
DOI: 10.6075/j05x28mf
title: CIL: 54429, Homo sapiens. In Cell Image Library

description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human non-symptomatic 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.