cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0ht2ns9
title: CIL: 51227, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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: 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: 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/j03b5xv3
title: CIL:13389, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: microscopy
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of a specific nucleic acid sequence
Visualization methods: Cy5; EGFP
Data qualification: Processed;spatialmeasurements
description: This image is one of a group of 4 images that supports the conclusion that hRio2 kinase activity is required for cytoplasmic 18S-E pre-rRNA processing. This image shows the distribution of all 18S rRNA precursors (white), via fluorescence in situ hybridization (FISH) with a 5' ITS1 probe, upon depletion of a protein important in rRNA processing, hRio2, and subsequent attempted rescue by transfection with an EGFP-tagged kinase-dead version of hRio2, in Hela cells. Depletion of hRio2 leads to the accumulation of 18S-E pre-rRNA in the cytoplasm (white), and this is rescued only by WT hRio2 (a companion image in this group), but not by hRio2 protein that lacks kinase activity, seen here in green. Note that the 5' ITS1 probe shows the localization of all 18S rRNA precursors, but only 18S-E pre rRNA is detected in the cytoplasm. HeLaK cells were transfected with Rio2-d siRNA and then the rescue construct was transfected after 48 h of RNAi. Cells were fixed after 72 h of RNAi, followed by FISH analysis. In the set of four images in this group, FISH pictures were processed in parallel by enhancing levels, followed by setting gamma correction to 0.75.
DOI: 10.3929/ethz-c-000783137
title: Ultrafast Dynamics Across the Phase Transition of the Charge Density Wave in K0.3MoO3
DOI: 10.6075/j09z93jq
title: CIL:13398, Dendraster excentricus. In Cell Image Library

description: Microtubules in sand dollar embryo expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). Vegetal view, 28-cell sand dollar embryo show astral microtubules frequently cross spindle midplane before and during anaphase, approach within 1 µm of the equatorial surface before furrowing, and curve inward as the furrow ingresses. Sand dollar embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C, which is tolerated well. Corresponds to Fig 1B and second segment of Video 1 in J Cell Biol. 2009 Dec 14;187(6):831-45.
description: Preparation: living tissue
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: EGFP
Processing history: unprocessed raw data
DOI: 10.3929/ethz-c-000785177
title: Cavity modification of magnetoplasmon mode through coupling with intersubband polaritons
DOI: 10.6075/j0cf9p3c
title: CIL:36581, Xenopus laevis, fertilized egg. In Cell Image Library

description: This image is part of a large data set of Xenopus laevis eggs imaged at various times post fertilization (the first number of the file name corresponds minutes, eg 30_2 is 30 min post fertilization). The embryos are stained for alpha-tubulin (green) using a directly labeled B-5-1-2 antibody and DNA (red).
description: Preparation: methanol fixed tissue
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 epitope; distribution of a specific protein
Visualization methods: labeled primary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Images collected on a Zeiss LSM 710 confocal with a 10X 0.3 NA objective using 561 and 633 laser lines.
DOI: 10.6075/j04b3008
title: CIL:13401, Strongylocentrotus purpuratus. In Cell Image Library

description: Preparation: living tissue
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: EGFP
Processing history: unprocessed raw data
description: Eight-cell purple urchin embryo expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). The embryo was treated with 20 µM nocodazole at time 00:00. Within 2 min, most astral microtubules disassembled; remaining microtubules are randomly oriented and most end well short of the cortex. Even so, furrowing is accurate and timely. Purple urchin were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C, which is tolerated well. Corresponds to Fig 3A and first segment of video 3 in J Cell Biol. 2009 Dec 14;187(6):831-45.
DOI: 10.6075/j0hx1bd9
title: CIL:13381, Homo sapiens, mammary epithelium (MEC). In Cell Image Library

description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
description: The nucleolus during mammary epithelial differentiation and early mammary tumorigenesis. Quiescent 2D cultures of MCF-10.B2 cells were stained with ANA-N antibody to detect nucleoli (green) and counterstained with DAPI to delineate nuclei (blue). The stack shown is presented as a projected image in Fig 1A (quiescent) of Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens.
DOI: 10.6075/j0q81bsj
title: CIL:13387, Homo sapiens. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: microscopy
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific nucleic acid sequence
Visualization methods: Cy5
Data qualification: Processed
description: This image is part of a group of 4 images supporting the conclusion that hRio2 kinase activity is required for cytoplasmic 18S-E pre-rRNA processing. This image is the untreated control for the experiment and shows the distribution of all 18S rRNA precursors (white), via fluorescence in situ hybridization (FISH) with a 5' ITS1 probe, in Hela cells. For the set of four images in this group, FISH pictures were processed in parallel by
enhancing levels, followed by setting gamma correction to
0.75.
DOI: 10.6075/j02j6b57
title: CIL:40703, Cricetulus griseus, epithelial cell. In Cell Image Library

description: Preparation: chemically fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: High voltage (1MeV) transmission electron microscopy image of a 0.5 micrometer section of a Chinese hamster ovary cell in metaphase containing a longitudinal section of a chromatid pair, and revealing the fiber-like structure. The image was taken with a specimen tilt of 55 degrees. Grouped with it is an image with a tilt of 45 degrees, providing a pair that affords an oblique stereo view of the chromosome.
description: Cells in metaphase were fixed, embedded in plastic, and 0.5 um sections cut and stained with uranyl acetate.
See also:
H. Ris 1981 Steroscopic electron microscopy of chromosomes. Meth Cell Biol 22:77-96
H. Ris 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:220-246.
DOI: 10.6075/j0rf5t68
title: CIL:13196, Haemanthus katharinae, endosperm. In Cell Image Library

description: Preparation: formaldehyde 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: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
DOI: 10.6075/j0xg9qb7
title: CIL:13194, Haemanthus katharinae, endosperm. In Cell Image Library

description: Dividing cells from the liquid endosperm of the lily Haemanthus katherinae were fixed with paraformaldehye, embedded in epoxy, and 1.0 micrometer sections prepared. Images were obtained with the Wisconsin high voltage TEM at 1MEV. For this low magnification survey micrograph of chromosomes at anaphase, the grid was tilted to 60 degrees. A similar micrograph tilted to 40 degrees is grouped with this image, making a stereo pair that provides an oblique 3D view.
description: Preparation: formaldehyde 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: elastic scattering of electrons
Visualization methods: uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j0bz64sf
title: CIL:13385, Homo sapiens, mammary epithelia (MEC). In Cell Image Library

description: FISH detection of PTEN and VEGF gene loci in MCF-10.B2 cells during mammary epithelial differentiation and early mammary tumorigenesis. PTEN (red) and VEGF (green)were detected in paraformaldehyde fixed MCF10A.B2 cells grown for 20 days under 3D growth conditions with 10 days of constitutive activation of ErbB2. DAPI (blue) delineates nuclei. A representative acinus structure is shown. The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens at zoom level 3. Optical sections imaged totaled approximately 15-20 microns in thickness.
See Fig 2 in Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
DOI: 10.6075/j08g8jf7
title: CIL:13380, Homo sapiens, mammary epithelium (MEC). In Cell Image Library

description: The nucleolus during mammary epithelial differentiation and early mammary tumorigenesis. Proliferating 2D cultures of MCF-10.B2 cells at day 0 were stained with ANA-N antibody to detect nucleoli (green) and counterstained with DAPI to delineate nuclei (blue). The stack shown is presented as a projected image in Fig 1A (Day 0) of Meaburn and Misteli, 2008 J Cell Biol 180:39-50.
The z-series was recorded with a Zeiss LSM 510 META confocal microscope with a 63x 1.4 NA objective lens.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Alexa Fluor 488; 4',6-diamidino-2-phenylindole (DAPI)
Processing history: unprocessed raw data
DOI: 10.6075/j0jh3jvj
title: CIL:13431, Homo sapiens, breast. In Cell Image Library

description: FISH detection of FOLS2 (FRA2; fluorescein, green) and CSF1R (rhodamine, red) in normal breast tissue. Nuclei counterstained with DAPI (blue). Tissue was fixed in formaldehyde, embedded in paraffin, and 4-5 micron sections cut. Stained sections were viewed using an Olympus IX70 microscope with a 60x 1.4 NA objective lens, and images acquired with a Photometrics CoolSnap CCD with a 1024X1024 pixel resolution, with a pixel size equivalent to 0.07427 microns in X and Y. Z-stacks were acquired to cover the thickness of the tissue section with a step size of 0.5 microns in the Z-direction, and subjected to deconvolution using SoftWoRx 3.5.1 software. A projection of the stack is included in this image group.
 Part of this field of view is shown in Fig 1A of Meaburn et al., 2009, J Cell Biol 187:801-812.
description: Preparation: formaldehyde fixed tissue; tissue in paraffin embedment
Relation to intact cell: microtome-sectioned tissue
Item type: charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain
Visualization methods: Rhodamine; Fluorescein (FITC); 4',6-diamidino-2-phenylindole (DAPI)
Processing history: 3D-deconvolution
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j0qz28q3
title: CIL:13402, Strongylocentrotus purpuratus. In Cell Image Library

description: Preparation: living tissue
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: EGFP
Processing history: unprocessed raw data
description: Eight-cell purple urchin embryo expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). The embryo was treated with 20 µM nocodazole at time 00:00. Purple urchin embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C, which is tolerated well. Movie corresponds to second segment of Video 3 in J Cell Biol. 2009 Dec 14;187(6):831-45.
DOI: 10.6075/j0vt1qrd
title: CIL:28752. In Cell Image Library

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.45 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. 
Recommended citation "We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j08p5z60
title: CIL:13399, Dendraster excentricus. In Cell Image Library

description: Preparation: living tissue
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: EGFP
Processing history: unprocessed raw data
description: Microtubules in sand dollar embryo expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). Eight-cell sand dollar embryo; single microtubules grow as far as the cell surface in all directions (equatorially in the 01:56 frame, tropically in the 01:08 frame, and toward the pole in the 03:32 frame). Astral microtubules reach the polar cortex most densely in anaphase (08:48) but also reach the equator before furrowing (frame 10:48). Embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C, which is tolerated well. Video corresponds to Fig 1C and third segment in Video 1 from J Cell Biol. 2009 Dec 14;187(6):831-45.
DOI: 10.6075/j0125rbx
title: CIL:13388, Homo sapiens. In Cell Image Library

description: This image is one of a group of 4 images that supports the conclusion that hRio2 kinase activity is required for cytoplasmic 18S-E pre-rRNA processing. This image shows the distribution of all 18S rRNA precursors (white), via fluorescence in situ hybridization (FISH) with a 5' ITS1 probe, upon depletion of a protein important in rRNA processing, hRio2, and subsequent rescue by transfection with an EGFP-tagged WT hRio2, in Hela cells. Depletion of hRio2 normally leads to the accumulation of 18S-E pre-rRNA in the cytoplasm (white), but this is rescued here by expression (green) of the transfected WT gene. Note that the 5' ITS1 probe shows the localization of all 18S rRNA precursors, but only 18S-E pre rRNA is detected in the cytoplasm. HeLaK cells were transfected with Rio2-d siRNA and then the rescue construct was transfected after 48 h of RNAi. Cells were fixed after 72 h of RNAi, followed by FISH analysis. In the set of four images in this group, FISH pictures were processed in parallel by enhancing levels, followed by setting gamma correction to 0.75.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: microscopy
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of a specific nucleic acid sequence
Visualization methods: Cy5; EGFP
Data qualification: Processed
DOI: 10.6075/j06m35hf
title: CIL:13397, Strongylocentrotus purpuratus. In Cell Image Library

description: Microtubules in live urchin embryos expressing three tandem GFPs fused to the ensconsin microtubule-binding domain (EMTB-3G; Faire et al., 1999). Microtubules approach the cortex everywhere before anaphase onset (1 min, 30 s). During anaphase, just before furrowing, many astral microtubules penetrate both polar and equatorial cortex. Embryos were imaged with a laser scanning confocal microscope (Radiance 2000; Bio-Rad Laboratories) mounted on a compound microscope (E800; Nikon) using a 40× 1.3 NA Plan-Fluor oil lens. Room temperature was maintained at 14–17°C, which is tolerated well. Related to Figure 1 and video 1 of J Cell Biol. 2009 Dec 14;187(6):831-45.
description: Preparation: living tissue
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: EGFP
Processing history: unprocessed raw data
DOI: 10.6075/j0k64h7n
title: CIL:12858, Rattus rattus, glandular epithelial cell, milk secreting cell, mammary alveolar cell. In Cell Image Library

description: Preparation: cryostat-sectioned tissue; formaldehyde fixed tissue; embedded tissue; methylcellulose embedded
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; distribution of a specific protein
Visualization methods: gold; uranyl salt; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Tissue was processed for immunoelectron microscopy using a modified Tokuyasu method. Briefly, minced tissue was fixed in 4% paraformaldehyde containing 5% sucrose and 100 mM HEPES and infiltrated with PBS containing 2.1 M sucrose over 10 h, with repeated solution changes. Fixed tissue was transferred to an aluminum cryosectioning stub (Ted Pella, Inc., Redding, CA) and immediately frozen in liquid nitrogen. Semithin (90 nm) cryosections were cut at -110C with an UltraCut UCT/FCS cryomicrotome (Leica), using a diamond knife (Diatome) and transferred to a Formvar-coated, carbon-coated, glow-discharged 100-mesh copper-rhodium electron microscopy grid. Following blocking of nonspecific antibody binding sites with 10% calf serum in PBS, the sections were labeled by incubation with an antibody to MG-160 (mouse monoclonal) followed by colloidal gold-conjugated secondary antibody (10 nm anti-mouse; Ted Pella Inc., Redding, CA) and then negatively stained and embedded with 1% uranyl acetate, 1% methylcellulose in distilled water. Samples were viewed in a Philips CM10 electron microscope, and images were collected digitally. See Ladinsky and Howell (2007) for more information on methods used.
description: Immunoelectron microscopy of mammary gland tissue from lactating rats with medial cisternae of the Golgi apparatus indicated by immunogold labeling of MG-160, a 160 kDa membrane sialoglycoprotein specific to medial Golgi.