cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j01836bm
title: CIL: 54722. In Cell Image Library

description: Item type: EM tomogram
Imaging mode: EM Survey
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 is a 2D survey mosaic of cerebral cortex.
DOI: 10.6075/j0xs5v74
title: CIL: 54652, 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, 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 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/j0w66knd
title: CIL: 54790, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Confocal fluorescent imaging
description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: DAPI staining
DOI: 10.6075/j0445mbw
title: CIL: 54697, 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: sfGFP with TIR-EVLO site.
DOI: 10.6075/j0br8s2k
title: CIL: 54674, 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, 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 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: 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/j02b8xs1
title: CIL: 54596, 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: 10.6075/j0bv7gcj
title: CIL: 54483, 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 amyloid-beta (4G8).
description: Imaging mode: bright-field microscopy
Visualization methods: 4G8 IHC using HRP/DAB
DOI: 10.6075/j0dz085c
title: CIL: 54623, Mus musculus, oocyte. In Cell Image Library

description: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
description: FIG.2C 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).
DOI: 10.6075/j0c24w9v
title: CIL: 54609. In Cell Image Library

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

The antenna was imaged using a Zeiss Gemini scanning electron microscope equipped with a Gatan 3View2XP and OnPoint backscatter detector. Images were acquired at 2.5 kV accelerating voltage with a 30 μm condenser aperture and 1.5 μsec dwell time; Z step size was 50 nm; pixel size was 6.48 nm; raster size was 12k x 9k; Z dimension was 1444 sections, and local gas injection was set to 85%. Volume was aligned using cross correlation, segmented, and visualized using IMOD.
DOI: 10.6075/j0cz3710
title: CIL: 54635, 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: Imaging mode: whole mount confocal image
Visualization methods: Laser Scan Confocal; PMT
description: FIG. 4A Changes in cortical ER clusters at the site of sperm binding and incorporation.
DOI: 10.6075/j08k7905
title: CIL: 54751, 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/j0513zhs
title: CIL:57185, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Scan 01_B_TI_A -- 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. Files may be viewed and annotated using standard, open source slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
DOI: 10.6075/j06973r5
title: CIL:57518, Aedes aegypti Maxillary Palp. In Cell Image Library

description: Sample Preparation and Imaging Overview:

Following the CryoChem protocol (Tsang et al., 2018), a Aedes Aegypti maxillary palp was prepared for high-resolution volume EM. The maxillary palp was isolated, cryofixed using high-pressure freezing, and processed through freeze-substitution, rehydration, en bloc heavy metal staining, dehydration, and Durcupan resin infiltration.

Microcomputed X-ray tomography was used to orient the sample, which was subsequently mounted on an aluminum pin with conductive epoxy and sputter-coated with gold-palladium. Imaging was performed using a Gemini SEM 300 (Zeiss) equipped with a Gatan 3View2XP system and an OnPoint backscatter detector. The SBEM imaging parameters included 2.5 kV accelerating voltage, 30-μm aperture, 1 μs dwell time, 5 nm per pixel resolution, and 40 nm Z-step size. To minimize charging artifacts, focal charge compensation with nitrogen gas was applied.
description: In 2018, the Su and Ellisman group developed a novel electron microscopy technique called CryoChem, designed to achieve optimal morphological preservation of genetically labeled tissues. To evaluate the preservation quality provided by CryoChem, we performed Serial Block-Face Scanning Electron Microscopy (SBEM) on CryoChem-processed Maxillary Palp.
description: Imaging mode: serial block face SEM (SBFSEM)
DOI: 10.5281/zenodo.17490236
title: Ctagger
DOI: 10.5281/zenodo.17490237
title: Ctagger
DOI: 10.6075/j0n58mk5
title: CIL:57519, Drosophila melanogaster Antenna, Olfactory receptor neurons. In Cell Image Library

description: Sample Preparation and Imaging Overview:

Following the CryoChem protocol (Tsang et al., 2018), a Drosophila melanogaster antenna expressing membrane-tethered APEX2 in ab4A ORNs (Or7a GAL4 driver) was prepared for high-resolution volume EM. The antenna was isolated, cryofixed using high-pressure freezing, and processed through freeze-substitution, rehydration, en bloc heavy metal staining, dehydration, and Durcupan resin infiltration.

Microcomputed X-ray tomography was used to orient the sample, which was subsequently mounted on an aluminum pin with conductive epoxy and sputter-coated with gold-palladium. Imaging was performed using a Gemini SEM 300 (Zeiss) equipped with a Gatan 3View2XP system and an OnPoint backscatter detector. The SBEM imaging parameters included 2.5 kV accelerating voltage, 30-μm aperture, 1 μs dwell time, 5 nm per pixel resolution, and 40 nm Z-step size. To minimize charging artifacts, focal charge compensation with nitrogen gas was applied.
description: In 2018, the Su and Ellisman group developed a novel electron microscopy technique called CryoChem, designed to achieve optimal morphological preservation of genetically labeled tissues. To evaluate the preservation quality provided by CryoChem, we performed Serial Block-Face Scanning Electron Microscopy (SBEM) on CryoChem-processed Drosophila antenna.
description: Imaging mode: serial block face SEM (SBFSEM)
DOI: 10.6075/j0n29x9n
title: CIL:57192, Homo sapiens. In Cell Image Library

description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPES was added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
description: Imaging mode: scanning electron microscopy (SEM)
DOI: 10.6075/j0wh2qbm
title: CIL:57193. In Cell Image Library

description: Imaging mode: STEM Tomography (⨉40k)
description: Primary Cell Culture
description: DIV10 torsinA-KO neuron
DOI: 10.6075/j0cj8dt4
title: CIL:57191, Homo sapiens. In Cell Image Library

description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPES was added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
description: Imaging mode: scanning electron microscopy (SEM)
DOI: 10.6075/j08s4q76
title: CIL:57184, Homo sapiens. In Cell Image Library

description: Scan 01_A_CA_A -- 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. Files may be viewed and annotated using standard, open source slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
DOI: 10.6075/j07s7p3t
title: CIL:57189, Homo sapiens. In Cell Image Library

description: Fibrin clots were generated by incubation of healthy donor plasma with or without SARS-Cov2 Spike protein in the presence of thrombin. After clot formation, SEM imaging was performed and 4000X images were captured across the sample.
description: Imaging mode: scanning electron microscopy (SEM)
description: Healthy donor citrated human plasma was diluted 1:3 in 20 mM HEPES buffer, pH 7.4; 15 μl of the diluted plasma was mixed with 15 μl of recombinant trimeric Spike protein that was buffer-exchanged into 20 mM HEPES and 137 mM NaCl using Amicon concentrators (100 kDa cut-off) prior to addition to plasma.Low concentration of NaCl was used to maintain Spike solubility and stability.Then, 25 μl of this mixture was pipetted onto 5 mm x 5 mm silicon wafers (Ted Pella) and incubated for 15 minat 37 °C in a humidified tissue culture incubator. Next, 25 μl of a solution of CaCl2 and thrombin in 20 mM HEPES was added in the center of the wafer and allowed to polymerize at 25 °C for 2 h. Final concentrations were plasma 1:12, 0.9 μM Spike, 0.25 U/ml thrombin, 20 mM CaCl2. Buffer was used instead of Spike for vehicle control. Clots on wafers were placed on ice, washed twice for 10 min each with ice-cold electron microscopy grade 0.1 M cacodylate buffer, pH 7.4,and fixed with cold electron microscopy grade 2% glutaraldehyde (Electron Microscopy Sciences). Samples were rinsed three times for 5 min each in Millipore-filtered, double-distilled water; dehydrated in an ethanol series (20%, 50%, 70%, 90%, 100%, 100% for 2 min each); and critical point dried with CO2. Samples were sputter coated with a thin layer of gold-palladium and imaged with a Zeiss Merlin field-emission scanning electron microscope at 3.0 keV and a secondary electron detector.
SEM imaging and image acquisition were carried out blinded to test conditions. 4000X images were captured across the sample, then were converted to 8-bit with NIH ImageJ (v. 1.50). After pixel to micron scaling, each image was cropped into two or three fields of view (FOV) (8×8 μm) with NIH DiameterJ. Surface plot plug-in ImageJ was used to generate topographical maps of SEM images. Briefly, the best segmentation algorithm was pre-selected based on side-by-side comparison of images before quantification. The Mixed Segmentation (M1-through M3 options) built in DiameterJ Segment provided the most accurate representation of the fibers to be quantified. The same segmentation method and variant was used across all test conditions and images. Each segmented image was manually edited with ImageJ to ensure complete representation of segmented fibers. Edited images were batch processed with DiameterJ 1-108 (orientation analysis not selected). Fiber radius and intersection densities were collated from each batch.
DOI: 10.6075/j00c4w3v
title: CIL:57196. In Cell Image Library

description: Primary Cell Culture
description: DIV10 WT neuron
description: Imaging mode: STEM Tomography (⨉40k)
DOI: 10.6075/j0rv0p1m
title: CIL:57194. In Cell Image Library

description: Imaging mode: STEM Tomography (⨉40k)
description: DIV10 WT neuron
description: Primary Cell Culture
DOI: 10.6075/j01836tw
title: CIL:57195. In Cell Image Library

description: Imaging mode: STEM Tomography (⨉40k)
description: Primary Cell Culture
description: DIV10 torsinA-KO neuron