cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0gm874q
title: CIL:36932, 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 an image of an immature neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. 
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the 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/j0c8280p
title: CIL:13699, Chlorocebus aethiops. In Cell Image Library

description: This is one of a group of four images in Figure S5 in Apaja et al., JCB 2010, that support the conclusion that the WT vasopressin type2 receptor (V2R) and the V2R W164S mutant (that causes nephrogenic diabetes insipidus) have different post-endocytic targeting. The sorting of endocytosed myc-tagged WT and W164S V2R was determined by indirect immunolabeling of internalized receptors in transiently transfected COS7 cells. The WT and temperature (26 degrees C) rescued mutant receptors were labelled with anti-myc Ab in live cells (1h) and then chased in Ab-free medium (1h, 37 degrees C) before indirect immunolabeling. Endosomes were labeled with 10 µg/ml Alexa Fluor 594–transferrin uptake for 1 h at 37°C. Fluorescence micrographs were obtained by a microscope (LSM510 or LSM710; Carl Zeiss, Inc.) equipped with a Plan-Apochromat 63×/NA 1.4 objective in multitrack mode. This single optical section shows that the internalized V2R W164S mutant is not found in endosomes, the normal location of endocytosed WT V2R. Companion images show that the mutant V2R, however, is found in lysosomes.
description: Preparation: crosslinking-fixative 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 a specific protein
Visualization methods: Alexa Fluor 488; Alexa Fluor 594
Data qualification: Processed
DOI: 10.6075/j0ns0t7b
title: CIL:40388, Psidium guajava, epidermal cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; critical_point dried specimen; ethanol dehydration
Relation to intact cell: sectioned tissue
Item type: recorded image
Imaging mode: scanning electron microscopy (SEM)
Parameter imaged: elastic scattering of electrons
Source of contrast: differences in adsorption or binding of stain
Visualization methods: osmium tetroxide; shadowing and plating
Processing history: unprocessed raw data
description: Scanning electron microscope image of Psidium guajava epidermal surface of the stem, showing trichomes (hair-like projections).This image is part of a group on botanical stems (CIL:40378-40395).
description: Image collected on a Zeiss DSM 962 SEM. Complete specimen preparation protocol available at:
http://remf.dartmouth.edu:8080/EM-Wiki/36
DOI: 10.6075/j0r21150
title: CIL: 54494, Homo sapiens. In Cell Image Library

description: Pathology load assessment of de-identified, human, post-mortem Alzheimer's disease and age-matched non-symptomatic donor prefrontal cortex brain tissue. We used these imaging data to inform donor stratification when we generated a large single nuclei RNA sequencing (snRNA-seq) dataset. Given we generated both imaging and snRNA-seq datasets the same location/piece of tissue for each donor, this gives us an unprecedented platform to evaluate cell type/subpopulation transcriptomes and relate them directly to their respective tissue microenvironments.
description: Imaging mode: bright-field microscopy
Visualization methods: AT8 IHC using HRP/DAB
description: 5 um sections of FFPE prefrontal cortex tissue from post-mortem, human Alzheimer's disease donor labeled for phosphorylated tau (AT8).
DOI: 10.6075/j0891565
title: CIL:39535, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cdc6. Cdc 6 is an essential ATP-binding protein required for DNA replication, component of the pre-replicative complex (pre-RC) which requires ORC to associate with chromatin and is in turn required for Mcm2-7p DNA association; homologous to S. pombe Cdc18p.These phase,gfp z-series images are part of an image group that ranges from CIL:39531-39535. 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; visualization of contiguous regions
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j0wm1c30
title: CIL:19120, Spiroplasma kunkelii, Dalbulus maidis, epithelial cell, prokaryotic cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; permeabilized 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; distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody; Alexa Fluor 488; propidium iodide
Data qualification: Processed
description: Confocal laser scanning micrograph of immunofluorescence-labeled corn stunt spiroplasma (CSS, Spiroplasma kunkelii, Class Mollicutes) aggregates (green) in whole mount preparations of its leafhopper vector D. maidis, showing the Malpighian tubule (mt). Whole-mount organs were labeled with primary CSS antibodies then with secondary antibodies (Alexa Fluor-488, green), and stained with the nuclear stain propidium iodide (red). CIL:12582, from the same image group, is an unlabeled version of this image. CSS is a wall-less procaryote that causes corn stunt disease and is biologically transmitted by some leafhopper species, e.g. Dalbulus maidis and D. gelbus (Hemiptera, Cicadellidae). Spiroplasma cells are limited by a unit membrane with no cell wall. They can be quasi-spherical, pleiomorphic or maintain a filamentous/spiral form. CSS multiplies in both plant and insect hosts and is transmitted with salivary secretions during feeding of the vector on new host plants. For additional information refer to Ammar and Hougenhout(2005) Ann. Entomol. Soc. Am. 98(6): 820Ð826.
DOI: 10.6075/j0610zr3
title: CIL: 51867, 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: 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.
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
DOI: 10.6075/j01n80bt
title: CIL:1784, Caenorhabditis elegans. In Cell Image Library

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
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.
DOI: 10.6075/j0xw4jx1
title: CIL:43413, Mus musculus, mammary adenocarcinoma. In Cell Image Library

description: Wound Healing Assay
Time series DIC images of mouse DA3 cells, derived from the mouse mammary adenocarcinoma cell line D1-DMBA-3, induced in BALB/C mice by dimethylbenzanthracene were grown to 90% confluence. A scratch approximately 300um wide was made in the cell monolayer, and images were recorded every 14.5 min for 26 hr.
This time series image, obtained with PHA and HGF/SF treatment, is part of a group of 17 time series images (CIL:43401 to CIL:43417) representing three different treatments: (1) no HGF/SF (CIL:43406 to CIL:43411), (2) with HGF/SF (CIL:43401 to CIL:43405), activating HGF/SF-Met signaling, and (3) with PHA (Met inhibitor) and HGF/SF (CIL:43412 to CIL:43417). The group also includes two movies (CIL:43418 and CIL:43419) created from the time series CIL:43402 and CIL:43406 respectively.
description: DA3 cells expressing the fluorescent protein mCherry were grown to 90% confluence in wells of 2 cm diameter in DMEM supplemented with 10% heat-inactivated FCS (Gibco-BRL) and treated with or without the Met inhibitor PHA665752 (2.5 µM) for 2 hrs. A scratch was generated using a 200 µl tip, and the cells were incubated with or without 80 ng ml-1 Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and subjected to time lapse confocal laser scanning microscopy (CLSM-510, Zeiss, Germany) for approximately 26 hrs, with images taken at 14.5 min intervals. The position of each scratch was predefined, and a macro that repetitively positions the microscope on each point was executed. The acquired differential interference contrast (DIC) channel of the time-lapse sequence (shown here) was used for the multi-cellular analysis; the red fluorescence channel was exploited for single cell tracking.
See also: Zaritsky A, Natan S, Ben-Jacob E, Tsarfaty I (2012). Emergence of HGF/SF -induced Coordinated Cellular Motility. PLOS ONE 7(9): e44671
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: 10.6075/j0p26x0s
title: CIL:40988, Rattus rattus, hepatocyte. In Cell Image Library

description: Transmission electron micrograph of a thin section of plastic-embedded material from the 'rough microsome' fraction of a preparation of rat liver. Subsequent to this early image, 'microsomes' became known as ribosomes, and the subcellular fraction consisting of membrane fragments studded with ribosomes became termed rough endoplasmic reticulum, the site of synthesis of proteins destined for export from the cell.
description: Preparation: chemically fixed tissue; tissue in plastic embedment
Relation to intact cell: isolated subcellular component; 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
Data qualification: Processed
description: Original 3.25 in. x 4 in. lantern slides were scanned at 600dpi.
DOI: 10.6075/j06q1whd
title: CIL:1700, 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: 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: 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.
DOI: 10.6075/j0gm86k4
title: CIL:1009, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 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: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
DOI: 10.6075/j07s7nwq
title: CIL:40026, Caulobacter crescentus CB15, prokaryotic cell. In Cell Image Library

description: A maximum intensity projection of a Caulobacter crescentus specimen at 0 degree tilt.
description: Preparation: acrolein fixed tissue; glutaraldehyde fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Parameter imaged: electron density
Data qualification: Processed
description: Caulobacteria were induced for 1 hour at 30 degrees C, labeled in M2G medium for 2 hours at 30 degrees C (in the presence of 1.8 micromolar ReAsH-EDT2) and photoconverted.

Samples were fixed with 2.5% glutaraldehyde with 1% acrolein in 0.05M sodium cacodylate pH 7.4 with 3 mM CaCl2 and 1 % sucrose followed by conventional osmium tetroxide/potassium ferrocyanide post-fixation, dehydration and embedding, and sectioning at 4µm thickness. A single tilt series of images were acquired using a JEOL 4000, from -60 to 60° at 2° increments, magnification, 40000.0.
DOI: 10.6075/j0s46r5k
title: CIL:2184, Caenorhabditis elegans. In Cell Image Library

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 4 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: 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: 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/j04j0dtx
title: CIL: 54043, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: STE family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.21227/6ptp-xq60
title: "ROAM-EMG"

description: "Dataset for ReactEMG."
DOI: 10.6075/j0rf5snp
title: CIL:45931, 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 25854 - 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.