cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0k64gm5
title: CIL:46258, Homo sapiens. In Cell Image Library

description: Gustafsdottir et al. (doi:10.1371/journal.pone.0080999) have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.

Using the cell-painting assay, the Broad Institute has assembled a reference dataset of profiles for U2OS osteosarcoma cells treated with ~30,000 compounds. The compound collection includes DOS-derived compounds (20,000), as well as chemically diverse MLI compounds with biologically diverse performance identified through analysis of PubChem (10,000), and known bioactive compounds to serve as landmarks (2,500). The DOS compounds consist of structurally diverse and stereochemically rich compounds with structures distinct from the current MLSMR. The compound collection also includes 267 distinct compounds nominated by MLPCN Centers from projects for which the Centers would like to identify new chemical series with similar activities.

The experiment consists of 413 microtiter plates. Each plate has 384 wells. Each well has 9 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.
description: Plate 26118 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
DOI: 10.6075/j0ws8s3b
title: CIL:44153, Mus musculus, lymph node. In Cell Image Library

description: Imaging was performed using a Leica TCS SP5-AOBS 5-channel confocal/two photon system equipped with multiline Argon, diode 561 nm, HeNe 594 nm and HeNe 633 nm as well as TiSaph two photon laser. Images were recorded with a 25x 0.95 NA water dipping objective lens, and 5 micrometer z-spacing and processed using Imaris (Bitplane). 
See also: Malide D, Metais J-Y, and Dunbar CE. (2012). Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
description: The picture represents a 3D-reconstruction (using Imaris software) of confocal/multiphoton (Leica SP5) images collected through the thickness (100 micrometers) of a live lymph node from a bone-marrow transplanted mouse. Cells marked by five fluorescent proteins: Cerulean (cyan), EGFP (green), Venus (yellow), tdTomato (purple), mCherry (red) appear surrounded by collagen matrix (second harmonic generation-SHG, white) at 4 months post-transplant. 
 See also Malide et al. (2012) Dynamic clonal analysis of murine hematopoietic stem and progenitor cells marked by 5 fluorescent proteins using confocal and multiphoton microscopy. Blood. Dec 20;120(26):e105-16.
 
 This is one of three grouped images obtained using the same imaging strategy.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy; multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: compartmentalization of stain or label
Visualization methods: CeruleanFP; EGFP; VenusFP; tdTomatoFP; mCherryFP; second harmonic generation SHG
Data qualification: Processed
DOI: 10.6075/j0f76bzv
title: CIL:44501, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h. CIL:44511 contains a movie of the process.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.
description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
description: Preparation: living tissue
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: 10.15468/dl.rfbvjb
title: Occurrence Download

description: A dataset containing 1092 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Checklist of Serengeti Ecosystem Grasses"
 ]
}

 The dataset includes 1092 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009679-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0wq0357
title: CIL:44506, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.
description: Preparation: living tissue
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
description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
DOI: 10.6075/j0ms3s5v
title: CIL:44502, Canis lupus familiaris, kidney epithelial cell. In Cell Image Library

description: Preparation: living tissue
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
description: Time series light microscopy images illustrating a wound healing assay. A monolayer of MDCK (Madin-Darby Canine Kidney) epithelial cells is scratched to create a 'wound' about 300 micrometers in width, after which the growth of the cells to fill the wound is monitored by recording images over the course of 15h.This image is part of a group of 12 that includes control cells (CIL:44501, 502, 506, 507, 508) and after addition of Hepatocyte Growth Factor /Scatter Factor (HGF/SF) to activate HGF/SF-Met signaling (CIL:44503, 504, 505, 509, 510). Also in the group are two movies, one control (CIL:44511), and one HGF/SF treated (CIL:44512). For additional wound healing assays see CIL:43401 and images grouped with it.
description: Madin-Darby Canine Kidney (MDCK) epithelial cells expressing YFP-membrane were maintained in DMEM supplemented with 5% fetal FCS in a 37°C, 5% CO2 incubator.
Wound healing assay: Cells were grown to 90% confluence in 24-well plates. Prior to scratching, the cells were starved by changing the medium to DMEM plus 0.1% FCS (starvation medium) for 24 hours. The medium was then changed to either fresh starvation medium (control), or starvation medium with 80 ng ml-1 HGF/SF for an additional 2 hours. A scratch of approximately 300 μm in width was generated using a 200 μl tip. The plate was subjected to time lapse microscopy in a stage incubator (OKOLAB, Italy) on a computer-controlled motorized stage of a confocal microscope (CLSM-510, Carl Zeiss, Germany), used in non-confocal DIC mode, with a 10x (NA 0.30) objective. Image acquisition was initiated 2 hours post scratching. Images were acquired every 15.7 minutes for 15 hours. The coordinates of each scratch were predefined, and a macro that repetitively positions the field of view at each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence was used for the analysis.
DOI: 10.6075/j0154fw1
title: CIL:41812, Coprophilous fungi. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: epi-illumination
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: composite of stacked images
description: This image of dung (Coprophilous) fungi found on a cow pile is composed using 20 stacked images that were captured with epi-illumination. Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j0n015d5
title: CIL:41811, Cyanobacteria, Oryza. In Cell Image Library

description: Confocal micrograph of cyanobacteria (red) growing on rice plant roots (green). Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
DOI: 10.6075/j02n5155
title: CIL:41810, Tinca tinca, scale. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: oblique illumination
Parameter imaged: absorption of illumination
Source of contrast: differences in intrinsic optical density
Visualization methods: visualization of contiguous regions
description: Scale detail of Tench fish (Tinca tinca) from Russian lakes. This image was captured using oblique transmitted light. Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j03f4ngh
title: CIL:41809, Gallus gallus domesticus. In Cell Image Library

description: Fluorescently-labeled actin from chicken muscle. Actin is a protein involved in muscle contraction and cell movement. Purified actin can form loose bundles that self-organize into regular patterns. Image captured using total internal reflection fluorescence (TIRF) microscopy. Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
description: Relation to intact cell: isolated subcellular component
Item type: recorded image
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
DOI: 10.6075/j0cc0zgh
title: CIL:41825, Drosophila melanogaster, epidermal cell, sensory neuron. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Processing history: projection of confocal stacks
description: Confocal image stacks of Drosophila (fruit fly) larvae with labeled dendrite arborization sensory neurons and epidermal cells. In the vertical larva, green is dendrites of sensory neurons on the body wall and red is the posterior half of epidermal cells of every segment. In the horizontal larvae, in the top larva green is dendrites of sensory neurons on the body wall and red is attachment sites of body wall muscles. In the middle larva green is cell borders of epidermal cells and red is dendrites of sensory neurons on the body wall. In the bottom larva green and red are dendrites of two types of sensory neurons on the body wall. Honorable Mention, 2010 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j00v8bm9
title: CIL:41823, Micrasterias. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: darkfield illumination; polarized light illumination
Parameter imaged: elastic scattering of photons; retardance
Source of contrast: differences in amount of elastic light scattering; intrinsic birefringence
Visualization methods: visualization of contiguous regions
description: Desmid Micrasterias, a chlorophyceae alga of extraordinary 
 beauty, beginning to divide. Micrasterias have bilateral symmetry, with two mirror image semi-cells joined by a narrow isthmus containing the nucleus. Image captured using darkfield and polarized light. Honorable 
 Mention, 2010 Olympus BioScapes Digital Imaging 
 Competition©.
DOI: 10.6075/j0j9656j
title: CIL:41821, Bacillariophyta. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: dark-field microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
description: Darkfield illumination image of a diatom from a oamaru fossil. Honorable Mention, 2010 
 Olympus BioScapes Digital Imaging Competition©.
DOI: 10.6075/j05719vq
title: CIL:41835, Didymosphenia geminata. In Cell Image Library

description: Photomicrograph of arranged diatom valves from Didymosphenia geminata (Lyngbye) Schmidt collected alive in the Clark Fork River in Missoula, Montana, then cleaned and mounted by the photographer. This diatom has become infamous in the last decade for its invasive nature, now thought to be transported to rivers around the world on the felt soles of flyfishermen. It is referred to as "Didymo" or "Rock snot" and in life looks like a wet sheep's fleece attached to rocks on the river bottom. Once introduced, it can spread throughout a river drainage. The larger valves are approximately 150 x 45 microns. The image was captured using Carl Zeiss Jamin-Lebedeff transmitted light interference contrast with a 40x objective and paired condenser. Retouching with Photoshop CS4. Honorable Mention, 2010 Olympus Bioscapes Digital Imaging Competition©.
description: Item type: recorded image
Imaging mode: interference contrast
Parameter imaged: optical path length gradient
Source of contrast: boundaries between regions with different refractive index
Visualization methods: visualization of contiguous regions
Processing history: photoshop
DOI: 10.6075/j05x289d
title: CIL:43901. In Cell Image Library

description: Tomograms of specifically labeled connexin 43 (Cx43) gap junctions expressed in HEK293T. Cx43 was genetically tagged with GPF and APEX, an engineered plant peroxidase that reacts with hydrogen peroxide and diaminobenzidine to create a protein specific stain. Sections are cut perpendicular to the membrane plane (cross-section view).
description: Preparation: glutaraldehyde fixed tissue
Item type: recorded image
Parameter imaged: electron density
DOI: 10.6075/j03n22st
title: CIL:43851, Mus musculus, mammary epithelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; tissue in wax embedment
Relation to intact cell: microtome-sectioned 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: 4',6-diamidino-2-phenylindole (DAPI)
description: Mammary gland tissue from wildtype P17.5 mice was fixed in formaldehyde, embedded in wax, and sections immunostained for vimentin (red), beta-catenin (green), and DNA (DAPI, blue). Images were recorded using a Leica confocal microscope. 
See also: Chakrabarti et al. 2012. Elf5 inhibits the epithelial-mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2. Nat Cell Biol 14:1212-1222.
description: The image shows a section of a developing wildtype mouse mammary gland immunostained for vimentin (red), beta-catenin (green) and DNA (blue). This is an example of a control image for experiments demonstrating the functions of the Elf5 protein. See: Chakrabarti et al. 2012. Elf5 inhibits the epithelial-mesenchymal transition in mammary gland development and breast cancer metastasis by transcriptionally repressing Snail2. Nat Cell Biol 14:1212-1222.
DOI: 10.6075/j0hq402r
title: CIL:43759, Homo sapiens, epithelial cell. In Cell Image Library

description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: Hoechst 33342; EGFP; Alexa Fluor 594
Data qualification: Processed;spatialmeasurements
description: Shown is a fluorescence microscopy image of a HeLa cell at mitotic metaphase. The cell is stained to reveal DNA (blue), microtubules (red), and the C-terminal portion of the KIF2A protein (green) which is largely confined to the compact chromosomes.
The image is part of a large project to characterize the locations of recombinantly tagged kinesin and myosin genes expressed from human or mouse-derived bacterial artificial chromosomes (BACs) as a resource for cell biology research. 
See also: Maliga et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nature Cell Biol; published online Feb 2013;DCI:10.1038/ncb2689.
description: HeLa cells carrying the appropriate EGFP-labeled transgene were fixed in cold methanol, rehydrated, and treated with mouse antibody to alpha-tubulin and goat antibody to GFP followed by donkey-anti-mouse Alexa 594, donkey-anti-goat Alexa 488 and Hoechst 33342. Preparations were examined using a Zeiss Axioplan 2 widefield microscope with a 63x NA 1.4 objective lens. Images were recorded using a CCD camera (CS472-95, Hamamatsu). 
For further details see: Zaliga M et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nat. Cell Biol. published online Feb 2013;DCI:10.1038/ncb2689.
DOI: 10.6075/j0g73d09
title: CIL:438, Patiria miniata, sperm. In Cell Image Library

description: Transmission electron micrograph of unstained cryo-section of a sperm cell of the starfish Patiria miniata. Echinoderm sperm nuclei are unusual in that chromatin fibers are clearly seen, allowing their diameter to be accurately determined.
 Cryosections of frozen material are typically of low contrast and show defects such as knife marks and compression. Despite these defects, individual chromatin fibers are clearly visible.
description: Whole sperm from the starfish P. miniata were cryo-fixed by plunging into liquid ethane, thin cryosections prepared, and examined in the frozen hydrated state using a Philips CM12 TEM operated at 80KV. Low dose images were recorded on SO-163 film.
See also: Woodcock CL 1994 Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J Cell Biol 125:11-9.
description: Preparation: unfixed tissue; cryofixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image; film
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: electron density
Source of contrast: intrinsic mass distribution; defocus phase contrast
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data