cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0m32vm7
title: CIL:37005, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: This is IMAGE #8 (70 minutes) of a time lapse series contained with in this image group. It shows the dendritic arbor of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals over one hour and 10 minutes and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 These cells were transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j05b01wh
title: CIL: 50932, Human mast cell line (HMC-1), Human mast cells. In Cell Image Library

description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
description: Wild type Human mast cell line 1 (HMC-1) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
DOI: 10.6075/j0w66jpf
title: CIL:38983, muscle cell. In Cell Image Library

description: B0003292 Mitochondrial inclusions in muscle biopsy. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: A transmission electron micrograph showing abnormal mitochondria with crystalline inclusions. This often occurs in hypermetabolic disorders and shows the disruption of normal mitochondrial structures. The crystals may be either ion crystals or protein crystals. This is a section through a muscle biopsy and clusters of contractile filaments are seen around the mitochondria.
description: Preparation: chemically fixed tissue
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Processing history: unprocessed raw data
DOI: 10.6075/j0639ntc
title: CIL:7747, Nassula, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: A high resolution view of cross-sectioned rows of basal bodies at the cortex of Nassula. Only a few basal bodies may have attached cilia as seen by the few cilia present in the upper right row. Basal bodies extend to the tips of the cytoplasmic mounds and each mound has a parasomal sac associated to one side. Unlike many other ciliates, the cartwheel occupies most of the basal body lumen. TEM taken on 4/1/69 by R. Allen with Philips 300 operating at 60kV. Neg. 14,800X. The raw film was scanned with an Epson Perfection V750 Pro. This image is available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm.

Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0513wxb
title: CIL:13736, Drosophila melanogaster, germ line cell, follicle cell, germ line stem cell, follicle stem cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: boi controls follicle stem cell proliferation. Germaria from boi[e] mutant in which germ cells (blue, anti-Vasa) and differentiating follicle cells (red, anti-Fas3) are labeled. Stalks between the germarium and the first budded egg chamber average 9 cells in wild type (CIL# 13735) and 18 cells in boi[e] mutants (see also CIL # 13737). Image correlates to Fig 1C in J Cell Biol. 2010. 191: 943-952.
description: Fly ovaries were dissected and fixed as described previously (O'Reilly et al., 2008). Primary antibodies were 1:2,000 rabbit anti-Vasa (Hay et al., 1990); 1:25 mouse anti-Fas3 (Developmental Studies Hybridoma Bank [DSHB]. Secondary antibodies used were either FITC, Cy3, and/or Cy5 conjugated to species-specific secondary antibodies (Jackson ImmunoResearch Laboratories, Inc.). Samples were mounted in Vectashield mounting medium. Images were collected at room temperature (22C) using 40× (1.25 NA) or 63× (1.4 NA) oil immersion lenses (Leica) on an upright microscope (DM 5000; Leica) coupled to a confocal laser scanner (TCS SP5; Leica). LAS AF SP5 software (Leica) was used for data acquisition. Images representing individual channels of single confocal slices from the center of each germarium were exported as TIFF files, and images were converted to figures using Photoshop software (Adobe).
DOI: 10.6075/j0r210bt
title: CIL:35650, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc20, a cell-cycle regulated activator of anaphase-promoting complex/cyclosome (APC/C) required for metaphase/anaphase transition; directs ubiquitination of mitotic cyclins, Pds1p, and other anaphase inhibitors; potential Cdc28p substrate novel protein thought to be involved in cell cycle regulation.These phase,gfp images are part of an image group that ranges from CIL:35640-35659. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: The images were acquired using a 60x 1.42 NA objective lens on Delta Vision system equipped with CoolSNAP_HQ2 / HQ2-ICX285. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0hh6j5d
title: CIL:24520, Rattus norvegicus, epithelial cell. In Cell Image Library

description: This image is one from a set of 40nm thick serial sections through part of a Golgi ribbon from a normal rat kidney cell, generated using transmission electron microscopy following incubation at 15°C to block transport out of the Golgi complex. Following temperature block, large bulging domains appear on the three trans-most cisternae. The images in this set were used in 3-dimensional reconstructions of the Golgi apparatus. For more information see: Ladinsky et al. (2002) Structure of the Golgi and distribution of reporter molecules at 20°C reveals the complexity of the exit compartments, Mol Biol Cell 13:2810-2825. The other images from this serial set are included in this image group.
description: Cells were grown on 100-mesh gold EM grids, and maintained at 15°C for 4 hours before plunge freezing in liquid nitrogen (BalTec HPM-010), followed by freeze-substitution (1% glutaraldehyde, 0.1% tannic acid in acetone, replaced with 4% osmium tetroxide and 0.01% uranyl acetate), then embedded in Epon-Araldite and sectioned at 40nm (UltraCut-UCT, Leica). Sections were transferred to formvar-coated copper-rhodium slot grids (EMS) and stained with 2% aqueous uranyl acetate and Reynold's lead citrate. Digital images were acquired at a magnification of 15,500X with an FEI Tecnai TF20 transmission EM. For additional details refer to: Mol Biol Cell 13:2810-2825.
description: Preparation: tissue in epoxy resin embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt
Processing history: unprocessed raw data
Data qualification: Processed
DOI: 10.6075/j0m32v79
title: CIL: 52106, Homo sapiens. In Cell Image Library

description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j0gx49f5
title: CIL:26558, Mus musculus, fibroblast. In Cell Image Library

description: Cells were cultured in DME (Invitrogen) supplemented with 10% fetal bovine serum and 100 U/ml penicillin/streptomycin (Invitrogen) at 37°C in a humidified 5% CO2 incubator. Cells were treated with 50 µM blebbistatin, 15min, fixed using 3.7% paraformaldehyde in PBS for 15 min, permeabilized using 0.2% Triton X-100 in PBS for 2 min, blocked with 2% BSA in PBS, and stained with the indicated primary antibodies for at 4°C overnight, followed by incubation with a secondary Alexa Fluor 488–, 546– or 594–conjugated antibody. F-actin was visualized with TRITC or Alexa Fluor 350–conjugated phalloidin. Images were captured by Leica TCS SP2 confocal microscope with HCX PL APO 63X objective.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Alexa Fluor 488; Alexa Fluor 546
Data qualification: Raw
description: To study the molecular mechanism by which nonmuscle myosin II (MII) regulates protrusion and adhesion dynamics in migrating cells, NIH3T3 cells were treated with 50 µm blebbistatin (BBS) for 15 min. and stained for βPIX (green) and myosin IIB (red). βPIX staining is transformed into numerous small puncta along the membrane after BBS treatment, and that myosin staining is excluded from the leading edge. These findings help elucidate a functional link between MII and Rac1/Cdc42 GTPases, which may regulate protrusion/adhesion dynamics in migrating cells. This image is the original data file from Fig. S4, “Potential involvement of βPIX in blebbistatin-induced morphological changes in MII-regulated cell protrusion and adhesion.” J. Cell Biol. 2010. Vol. 190(4):663–674.
DOI: 10.6075/j00c4vm5
title: CIL: 54699, Bacteria E coli, MC1061. In Cell Image Library

description: sfGFP with TIR-STD site.
description: Imaging mode: EPI on a Nikon TiE2 Hamamatsu ORCA Flash 4.0 sCMOS Camera and Nikon SR Apo TIRF 100x objective lens (NA 1.49)
description: Live cell bacterial imaging, expressing fluroescent protein in the cytoplasm.
DOI: 10.6075/j02806f4
title: CIL:11487, Sus scrofa, Leydig cell. In Cell Image Library

description: Figures 284 (upper) and 285 (lower) from Chapter 9 (Peroxisomes) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Diaminobenzidene reacts with peroxidase to produce a dense reaction product in the peroxisomes, distinguishing them from similarly shaped lysosomes in these images from Leydig cells of boar testis. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Data qualification: Processed
DOI: 10.6075/j06972fq
title: CIL:50603, Homo sapiens, monocyte. In Cell Image Library

description: Imaging mode: microscopy
Visualization methods: x100
description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: The monocyte type cell contained one erythrocyte.
DOI: 10.6075/j0862fzp
title: CIL: 52413, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=5, y=2, z=10 from BL024199_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/j0p26xpr
title: CIL: 52668, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=6, y=2, z=13 from PS09_287383C_Myc_Terc
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
DOI: 10.6075/j0pk0dz1
title: CIL:11056, Hirudinea, neuron associated cell (sensu Nematoda and Protostomia). In Cell Image Library

description: Transmission electron micrograph illustrating the unusually prominent fibrous nuclear lamina (arrows) seen in many invertebrates such as this leech ganglion cell. From Fawcett (1966) Am J. Anat. 119:129-146, and reprinted with permission as Figure 155 from Chapter 4 (Nucleus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
description: Preparation: tissue in plastic embedment; osmium tetroxide fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; osmium tetroxide; lead salt
Processing history: Image extracted from .pdf file of 'The Cell'
Data qualification: Processed
description: See: Fawcett DW 1966 On the occurrence of a fibrous lamina on the inner aspect of the nuclear envelope in certain cells of vertebrates. Am J Anat 119:129-145.
DOI: 10.6075/j0jd4wmw
title: CIL:36951, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
description: This is IMAGE #1 (day 1) of a time lapse series contained with in this image group. It is a pair of developing neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 The images were acquired daily over 3 days and show dendritic arbor development.
 
 The cells were transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j00v8bp6
title: CIL:38906, Escherichia coli, intestinal epithelial cell. In Cell Image Library

description: This pair of confocal micrographs demonstrates how a disease-causing strain of E. coli bacteria brings about diarrhoea by breaking down the waterproof barriers between the cells. The bacteria are seen as small red dots attached to the surface of intestinal cells making tiny pedestals out of one of the cell's own proteins (bright green). Once attached, the bacteria send signals into the cells, causing the tight junctions (blue) between the cells to break down. Water is then able to seep out between the cells into the intestine, leading to diarrhoea. The image on the left shows an early stage in the process where the tight junctions are still intact and show as continuous blue lines between the cells. The image on the right is taken later in the process, once the tight junctions have broken down. Their remnants appear as blue dots.
description: Preparation: chemically fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Processing history: unprocessed raw data
description: B0006873 Confocal micrograph 2007 Collection: Medical Photographic Library. Copyrighted work available under Creative Commons by-nc-nd 2.0 UK: England & Wales, see http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
DOI: 10.6075/j0fj2fkr
title: CIL:11366, Oniscus, invertebrate nurse cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; embedded tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed
description: Figures 201 and 202 from Chapter 6 (Golgi Apparatus) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. The Golgi apparatus of nurse cells from the testis of the woodlouse, Oniscus. Image by David Phillips. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0ht2pk1
title: CIL:55824, Homo sapiens. In Cell Image Library

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
description: Scan 01_H_CS_E -- 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, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.