cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j00001s5
title: CIL: 54440, 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 non-symptomatic donor labeled by Bielschowsky's silver stain.
description: Imaging mode: bright-field microscopy
Visualization methods: silver nitrate and ammonium hydroxide
DOI: 10.6075/j0qn66mb
title: CIL: 54763, 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/j0ww7hh2
title: CIL: 54630, Mus musculus, oocyte. In Cell Image Library

description: FIG. 3Bt, 3Beq Maturation of cortical ER clusters during different stages of fertilization.
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/j09z94rt
title: CIL: 54650, 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, 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 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/j0fx7996
title: CIL: 54803, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: Spheroid imaging
description: iRFP720 imaging of spheroids.
DOI: 10.6075/j0fq9wg5
title: CIL: 54647, 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 control D. melanogaster in the third instar larval stage, 62uM 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: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
DOI: 10.6075/j0028rdn
title: CIL: 54760, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: Nanog staining
description: Epifluorescent imaging
DOI: 10.6075/j0mg7pcq
title: CIL: 54640, Mus musculus, oocyte. In Cell Image Library

description: FIG. 4I Changes in cortical ER clusters at the site of sperm binding and incorporation.
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/j05d8rqp
title: CIL: 54626, Mus musculus, oocyte. In Cell Image Library

description: FIG.2F Changes in ER cluster morphology require gamete fusion.
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/j09p31cm
title: CIL: 54474, 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/j0hh6jx8
title: CIL: 54664, 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, 40uM 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
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/j0gh9hpj
title: CIL: 54478, 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 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/j00r9p89
title: CIL: 54821, Alysiella filiformis, bacteria. In Cell Image Library

description: Nikon Eclipse NI-U microscope equipped with a MFCool camera (Jenoptik).
description: A. filiformis filaments
description: Imaging mode: phase contrast microscopy
DOI: 10.6075/j0nz87hn
title: CIL: 54716. In Cell Image Library

description: Item type: recorded image
Imaging mode: Serial-section SEM
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.
DOI: 10.6075/j0xk8fdg
title: CIL: 54683, 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, 26uM 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/j0mg7p51
title: CIL: 54425, 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: 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.
DOI: 10.6075/j0154gkd
title: CIL: 52528, 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=20 from BL32077_Myc_Terc
DOI: 10.6075/j00v8cd1
title: CIL: 52974, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Image 5, z=4 from SC_011
description: One z layer of a z-stack at the given image
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/j0zk5g6c
title: CIL: 52451, 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=5, z=6 from BL32077_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/j0vq32f7
title: CIL: 54318, 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/j0ws8t46
title: CIL: 54660, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Confocal image of the CNS of a control D. melanogaster in the third instar larval stage, 70uM 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)
description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
DOI: 10.6075/j0hx1cjh
title: CIL: 54781, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Epifluorescent imaging
description: Imaging mode: fluorescence microscopy
Visualization methods: epifluorescent imaging
description: DAPI staining
DOI: 10.6075/j0k64hst
title: CIL: 54473, 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 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/j0ht2p5n
title: CIL: 54600, Mus musculus, Fetal Liver Macrophage. In Cell Image Library

description: Imaging mode: Lattice Light Sheet Microscope
Visualization methods: ChimeraX
description: Processed data
description: LY294002 treated
DOI: 10.5281/zenodo.17489749
title: ViTrace Detects Viral Signatures in Tumor Transcriptomes Using a Hybrid Language Model

description: The first simulated dataset, Sim1, was constructed by viRNAtrap. The training and testing data are randomly sampled from the simulated reads from hg19 reference genome and 13 virus species from 7 genera across 4 phyla. ViTrace and other 5 baseline models, viRNAtrap, DeepVirFinder, ViraMiner, DeepViFi, and Seq2Seq are all trained and tested on Sim1.

The second simulated dataset, Sim2, was constructed as an independent testing set to evaluate ViTrace's performance to identify viruses whose taxonomy had never been seen during the training.

The third simulated dataset, Sim3, was created to evaluate ViTrace’s ability to differentiate viruses from other microorganisms. Positive samples were generated from 12,567 viral genomes, covering 8,102 species across 1,012 genera, obtained from the NCBI RefSeq database. The negative samples were derived from balanced sequences representing bacteria, fungi, and archaea.

This mouse dataset originates from VVRD and NCBI GRC/m38, covering 7 microbial genera across 4 bacterial phyla.  It comprises 8.0 million samples for training, 800,000 for validation, and 2.91 million for testing, and is designed for training and testing purposes.
DOI: 10.6075/j0c53kd4
title: CIL: 52772, 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=7, y=2, z=12 from PS11_10021_2B_Myc_Terc
DOI: 10.5281/zenodo.15259038
title: ViTrace Detects Viral Signatures in Tumor Transcriptomes Using a Hybrid Language Model

description: The first simulated dataset, Sim1, was constructed by viRNAtrap. The training and testing data are randomly sampled from the simulated reads from hg19 reference genome and 13 virus species from 7 genera across 4 phyla. ViTrace and other 5 baseline models, viRNAtrap, DeepVirFinder, ViraMiner, DeepViFi, and Seq2Seq are all trained and tested on Sim1.

The second simulated dataset, Sim2, was constructed as an independent testing set to evaluate ViTrace's performance to identify viruses whose taxonomy had never been seen during the training.

The third simulated dataset, Sim3, was created to evaluate ViTrace’s ability to differentiate viruses from other microorganisms. Positive samples were generated from 12,567 viral genomes, covering 8,102 species across 1,012 genera, obtained from the NCBI RefSeq database. The negative samples were derived from balanced sequences representing bacteria, fungi, and archaea.

This mouse dataset originates from VVRD and NCBI GRC/m38, covering 7 microbial genera across 4 bacterial phyla.  It comprises 8.0 million samples for training, 800,000 for validation, and 2.91 million for testing, and is designed for training and testing purposes.
DOI: 10.6075/j04b30vg
title: CIL: 52442, 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=3, z=18 from BL024199_Myc_Terc
DOI: 10.6075/j0bk1cr6
title: CIL:57515, Mus musculus, FosDD-Cre. In Cell Image Library

description: Imaging mode: serial block face SEM (SBFSEM)
Visualization methods: APEX2-mGFP
description: Serial block face SEM volume of the mouse hippocampal CA1 stratum radiatum 7 days following contextual fear conditioning.
DOI: 10.6075/j0pc321v
title: CIL: 53454, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
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: 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/j0862g9k
title: CIL: 54634, Mus musculus, oocyte. In Cell Image Library

description: Oocytes fixed with 2% paraformaldehyde and 1% picric acid. Immunolabelled with anti-Calreticulin (green), Alexafluor 568-phalloidin (red), and Hoechst 33342 (blue).
description: FIG. 3Et, 3Eeq Maturation of cortical ER clusters during different stages of fertilization.
description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT