cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j03n22mk
title: CIL:1787, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 2 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: differential interference contrast microscopy
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0r49qb7
title: CIL: 52831, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: One z layer of a z-stack at the given tile position
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
description: Tile x=4, y=1, z=8 from PS11_167511L_Myc_Terc
DOI: 10.6075/j02j69pj
title: CIL:36072, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Data qualification: Processed
description: Figures 440 (upper) and 441 (lower) from Chapter 16 (Cytoplasmic matrix and cytoskeleton) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. Examples of the dense cytoskeletal network in the periphery of cells in vitro. In the upper panel, two microtubules traverse the meshwork of actin filaments. This cell was prepared by treated with Triton to extract soluble proteinaceous material, washed, quick frozen with liquid helium, deep etched, and rotary shadowed. Image by John Heuser. A PDF copy of the accompanying chapter is available on the ASCB‚Äôs BioEDUCATE website.
DOI: 10.6075/j0xg9pxf
title: CIL:40498, Homo sapiens, osteosarcoma. In Cell Image Library

description: Preparation: chemically fixed tissue; permeabilized 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
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw
description: The use of data and images from this site in publications and presentations is permitted provided that the following conditions are met:

The publication and/or presentation are solely for informational and non-commercial purposes.

The source of the data and/or image is referred to this site (www.proteinatlas.org) and/or the above publication is cited.
description: Single slice confocal images representing one optical slice of a cell stained for the Human Protein Atlas (HPA) antibody HPA043146 (shown in green). HPA043146 is a polyclonal Anti-INO80E antibody that labels the nucleus and the nucleoli in this cell line. The cells are also stained with reference markers in order to facilitate the annotation of the subcellular distribution of the protein targeted by the HPA antibody. The following probes/organelles are used as references; (i) DAPI for the nucleus (blue) and (ii) anti-tubulin antibody as internal control and marker of microtubules and (red).
DOI: 10.6075/j0pz58dw
title: CIL: 52868, Homo sapiens, High-grade serious overian cancer. In Cell Image Library

description: Tile x=4, y=5, z=3 from PS11_167511L_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/j04m9456
title: CIL: 53150, 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 image
description: Image 4, z=12 from SC_030
DOI: 10.6075/j04x5734
title: CIL:37388, damselfly, flight muscle cell. In Cell Image Library

description: Longitudinal and cross sections showing ribbon like myofibrils regularly alternating with layers of mitochondria and SR/T tubules. Dyads are located in a grove of the mitochondrial surface. Negatives aere scanned on nikon 8000 at 4000dpi/6.3 micron scan step size, then reduced in size 4X for upload, for an effective pixel size of 25 micron.
 
 Technical details:
 Heads and tail removed, thorax bisected and immersed in 3% glutaraldehyde buffered in 0.1 M cacodylate buffer (pH7.2). Stored at 4C for several days. Muscle dissected out. Rinsed 3Xin buffer, postfixed in 2% PsO4 in buffer, for 1.5 hrs; rinsed 3 times in water, en-block stained in saturated aqueous uranyl acetate, embedded in Spurr. Thin sections stained in uranyl acetate and lead and examined in a Philips 410 Microscope.
 
 Reference for the image:
Loesser, K.E., Castellani, L. and Franzini-Armstrong, C. Disposition of junctional feet in muscles of invertebrates. J. Muscle Research Cell Motility 13:161-173, 199
description: Preparation: glutaraldehyde fixed tissue; tissue in epoxy resin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
Processing history: digitized negative film
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0b56j22
title: CIL:39464, Vorticella convallaria, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Like other peritrichs the pellicle of Vorticella convallaria is sculpted into ridges and grooves that circle the cell perpendicular to the aboral/adoral axis of the cell body. Pellicular pores penetrate the pellicle as cylindrical indentations of the plasma membrane that end as clathrin-coated pits. A system of alveoli underlies the plasma membrane and rod-like densities occupy the cytosolic tips of the pellicular ridges. A fibrous epiplasm covers the inside of the alveoli. Distinct myonemal bands lie in the aboral to adoral direction to the inside of the epiplasm. These bands are associated with the endoplasmic reticulum by unique specializations of the ER. In this EM preparation the ER has artifactually segmented into vesicles caused by the fixation process. Mitochondria occupy the space between the bands. TEM taken on 4/15/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 9,250X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j00z72fd
title: CIL:12980, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: High magnification of early endosomes in which the membranes are easily seen as a tripartite track. Gold, labeling antigen C6 is observed only in the body of the early endosome and not in the coated evagination or small coated vesicle lying nearby, which may be a newly released carrier vesicle or a coated evagination still attached to an early endosome. TEM taken on 5/14/91 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. Bar = 0.2µm. Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are outlined in Methods Cell Biol. 2010;96:143-73. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12642) is in the library and available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0qz28s0
title: CIL:11620, Homo sapiens, ciliated epithelial cell, oviduct epithielial cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; critical_point dried specimen; whole mounted tissue; shadowing and plating
Relation to intact cell: whole mounted tissue
Item type: scanning electron microscopy (SEM); illumination by electrons
Imaging mode: secondary_electron imaging; film
Parameter imaged: secondary electron generation; secondary_electron imaging
Source of contrast: coherent illumination; secondary electron generation
Visualization methods: shadowing and plating
Processing history: recorded image; film; Scanned print from negative
Data qualification: Processed
description: Figure 317 from Chapter 13 (Cilia and Flagella) of 'The Cell' by Don W. Fawcett M.D. The inconsistent orientation of the cilia in scanning micrographs does not accurately reflect their state in the living cell. All of the cilia on a cell would normally be in the same phase of their cycle of beating. Routine methods of fixation are incapable of instantly immobilizing them in the attitude typical of their effective stroke or recovery phase. They therefore tend to come to rest in a more or less straight neutral position. A copy of the chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j05x27tq
title: CIL:36262, Vorticella convallaria, 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; Print from negative scanned for Photoshop.
Data qualification: Processed
description: A grazing section through the edge of the nuclear envelope. This illustrates nuclear envelope pores in face view. Polysomes, chains of ribosomes, are bound to the outer membrane of the nuclear envelope showing that this membrane is equivalent to rough ER as a site of protein synthesis for translocation across the membrane or for membrane protein synthesis. TEM taken on 2/5/72 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 28,500X. Bar = 0.2µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. There is a high resolution version of this image in the library (CIL:39454) which is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j0t72g6j
title: CIL:24803, Xenopus laevis, fibroblast. In Cell Image Library

description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Structural differentiation of actin network in lamellipodium. Electron micrograph of Xenopus fibroblast after unprotected extraction without polyethelene glycol and phalloidin. Actin network at lamellipodial rear disassembled in the course of unprotected extraction, whereas front zone remained as dense as in control cells (CIL 24801). Image corresponds to Figure 6f from J Cell Biol. 1999 May 31;145(5):1009-26.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cell in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; platinum replica
Processing history: unprocessed raw data
DOI: 10.6075/j01r6pnd
title: CIL:12084, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: A high resolution view of a median longitudinal section through this collecting canal that may be artificially swollen at two sites where it is encircled by structural microtubules. Smooth spongiome forms a mesh around the collecting canal and these microtubules. Decorated tubule bundles of the decorated spongiome are sparsely scattered peripheral to the smooth spongiome. TEM taken on 7/8/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 9,780X.
description: Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
DOI: 10.6075/j02v2fkf
title: CIL: 51741, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: Imaging mode: DICM
Visualization methods: Spinning disc confocal DICM & widefield DICM Using a Nikon TiE microscope equipped with a 40x, 0.95 N.A. objective and a Hamamatsu ORCA-Flash 4.0 V3 Digital CMOS camera, or a Nikon TiE spinning-disc confocal microscope equipped with a Yokogawa CSU-X1 scanning unit, an Andor iXon 888 EMCCD camera, and a 60x, 1.3 N.A. water-immersion objective or a 40x, 0.95 N.A. objective
description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

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: A novel cell population analysis to quantify both initial and long-term drug effects, namely pseudopod adaptation and recovery following an initial drug-induced perturbation, adding drug slowly in 1/4 increments over 90 minutes.
DOI: 10.6075/j02n521s
title: CIL: 54568, Xenopus Laevis, Entire Organism. In Cell Image Library

description: Video of African clawed frog embryonic development. Video filename format is as follows organism_temperature_batch. Data was collected at 13.6 degrees Celcius
description: Imaging mode: RGB
Visualization methods: Captured on a microscope using a Canon Rebel Ti5/6 or a one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 13.6 degrees C
DOI: 10.6075/j0x065zq
title: CIL:32140, Drosophila melanogaster, epithelial cell. In Cell Image Library

description: Drosophila melanogaster Kc167 cells were stained for DNA (to label nuclei, red) and actin (a cytoskeletal protein, to show the cell body, green). Each image is a dual channel fluorescent image followed by a line tracing of the nuclei and a line tracing of the cell boundary. These images are provided as a tool for testing algorithims to find nuclei and the boundaries between adjacent cells.

Chris Gang outlined the nuclei and cells.
Please use the following recommended citation when using this data. "We used the Drosophila Kc167 2 image set (Jones et al., Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications, 2005), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Images were acquired using a motorized Zeiss Axioplan 2 and a Axiocam MRm camera, and are provided courtesy of the laboratory of David Sabatini at the Whitehead Institute for Biomedical Research. Each image is roughly 512 x 512 pixels, with cells roughly 25 pixels in diameter, and 80 cells per image on average. 

Algorithms for finding boundaries between adjacent cells may use the union of the manually outlined cells as input. They may also use the manually outlined nuclei as seed regions. This ensures that the algorithms are compared according to their ability to find boundaries betwen adjacent cells, and not the orthogonal problems of segmenting nuclei and distinguishing foreground (cells) from background.

To compare an algorithm's results to the manual outlines, define the relevant boundary pixels as the pixels that are on the boundary found by the algorith and that are not adjacent to any background pixels. For each relevant pixel, compute the Euclidean distance to the corresponding pixel on the manually found outline. Report the percentage of relevant pixels that are within two pixels of the corresponding pixel on the manually found outline.
description: Relation to intact cell: dispersed cells in vitro
Item type: recorded image; hand drawn contour
Imaging mode: fluorescence microscopy
Parameter imaged: distribution of a specific protein; distribution of DNA
Source of contrast: distribution of a specific protein
Processing history: unprocessed raw data; tracing
Data qualification: Raw
DOI: 10.6075/j03777gm
title: CIL:50615, Homo sapiens, monocyte. In Cell Image Library

description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: One elongated monocyte-type cell contained several erythrocytes, one of them compressing the nucleus.
description: Imaging mode: microscopy
Visualization methods: x100