cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j09s1qp6
title: CIL: 53729, Homo sapiens, HeLa. In Cell Image Library

description: CMGC 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.
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: Visualization methods: confocal microscopy
DOI: 10.6075/j0x929t5
title: CIL: 52345, 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: Tile x=3, y=2, z=5 from BL024199_Myc_Terc
description: Imaging mode: Fluorescence in situ hybridization (FISH)
Visualization methods: Nikon Eclipse fluorescence inverted microscope equipped with a charge-coupled device camera (Andor Neo sCMOS), using filter sets for DAPI/ YGFP/TRITC/CY GFP with an objective lens (Plan Apo VC 100x, Nikon). Captured with 100x magnification of the objective and a pixel size of 0.07 microns
DOI: 10.6075/j03f4p2j
title: CIL: 50949. In Cell Image Library

description: Wild type Schizosaccharomyces pombe cells (cdc25-22) were high pressure frozen and visualized through transmission electron microscopy (TEM). The images show the nucleus of the cells and the black arrow indicates nuclear envelope budding events.
description: Imaging mode: transmission electron microscopy (TEM)
Visualization methods: Stain with Uranyl acetate and Lead citrate
DOI: 10.6075/j0zk5gs0
title: CIL:39993, Mus musculus, CNS neuron (sensu Vertebrata). In Cell Image Library

description: Mouse strain B6;129-/Slc6a3 tm2Mca was used in this preparation. Individual cells in fixed tissue were injected with Lucifer yellow and stored in 4% paraformaldehyde at 4° C. Fluorescence was photoconverted using DAB and a confocal laser light source. After this process, tissue was washed thoroughly in PBS and processed for EM by osmication, dehydration, and embedding in epoxy resin. For detailed methods, see the protocol provided in the CCDB. The tomogram was generated using an Hitachi UHVEM. Single tilt images spanned -60 to 60° in 2° increments. Magnification, 3000X; accelerating voltage, 3.0 MeV.
description: A spiny dendrite from neostriatum of a dopamine transporter knockout mouse. The cell was imaged using photoconverted Lucifer yellow, and a maximum intensity project image was created. This reconstructed image has been downsampled from the raw data image, which can be accessed using the link provided to the Cell Centered Database.
description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue; tissue in epoxy resin embedment; osmium tetroxide fixed tissue
Relation to intact cell: microtome-sectioned tissue
Item type: recorded image
Imaging mode: detection of electrons; illumination by electrons
Parameter imaged: electron density
Visualization methods: intracellular filling
Data qualification: Processed
DOI: 10.6075/j09w0f2g
title: CIL: 52842, 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=19 from PS11_167511L_Myc_Terc
DOI: 10.6075/j00p0xmk
title: CIL:45919, Homo sapiens. In Cell Image Library

description: Plate 25726 - 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.
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.
DOI: 10.6075/j0zp45vt
title: CIL: 54085, 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: TK 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: 10.6075/j0gb23hz
title: CIL: 51886, 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/j0708087
title: CIL:39025, Danio rerio, neuron. In Cell Image Library

description: B0007772 Dorsal view of a zebrafish brain. Wellcome Images available under the following creative commons usage http://creativecommons.org/licenses/by-nc-nd/2.0/uk/
description: Confocal micrograph of the brain of a transgenic zebrafish embryo. Some neurons express the green fluorescent protein (GFP) - shown in green under the control of a specific promotor. Tracts, axons and neuropils have been labeled using antibodies against tubulin (red) and synaptic vesicles (blue). The brain has been dissected out, removing skin and eyes. This image is a dorsal (back) view of the brain. CIL 39026 is the anterior view.
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; distribution of a specific protein
Visualization methods: EGFP; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j0639p58
title: CIL: 50746, Drosophila melanogaster. In Cell Image Library

description: We show in this study that brain and intestinal stem cells of Drosophila contain a new type of cytoplasmic protrusion which is enriched in mitochondria and that the mitochondria are probably dependent on microtubules for their distribution. The protrusions form mitochondria-enriched cytoplasmic bridges from the stem cells to their niche that we speculate are important in regulating stem cell quiescence and activation.
description: Specimen preparation: Larval brains (LBs) were prepared from starved (amino acid-restricted) first instar (L1) larvae to enrich for quiescent neural stem cells. The LBs were glutaraldehyde-fixed, tannic acid and OsO4-stained, embedded in resin, thin-sectioned (60-70 nm) and stained with uranyl acetate/lead citrate, then observed by TEM.
description: Item type: Digital
Imaging mode: CM12 TEM equipped with AMT digital camera
DOI: 10.6075/j0wh2nnt
title: CIL:27844. 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 0.0 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/j04f1qc5
title: CIL: 53683. In Cell Image Library

description: Visualization methods: confocal microscopy
description: CMGC 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.
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.
DOI: 10.6075/j0zk5fh0
title: CIL:11245, Felis catus, cardiac muscle cell. In Cell Image Library

description: Preparation: crosslinking-fixative fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: osmium tetroxide
Data qualification: Processed
description: Gap junctions in papillary muscle from cat heart. These communicating junctions are responsible for the spreading wave of depolarization through the myocardium. Desmosomes can also be found on the lateral surfaces of cardiac muscle cells, often near gap junctions. Figures 107 (upper) and 108 (lower) from Chapter 3 (Junctional Specializations) of 'The Cell, 2nd Ed.' by Don W. Fawcett M.D. A PDF copy of the accompanying chapter is available on the ASCB's BioEDUCATE website.
DOI: 10.6075/j0jd4wnb
title: CIL: 54685, Drosophila melanogaster, astrocytes (red). In Cell Image Library

description: Astrocyte-specific RFP expression was achieved using driven using the Gal4-UAS binary system and the driver alrm. Cortex-glia specific GFP was achieved using the lexA-lexAop binary system and the cortex-glia specific driver wrapper932i-LexA (Coutinho-Budd et al., 2017). The larval CNS was dissected in the third instar larval stage, fixed with methanol, stained for RFP, GFP and Elav (neuronal nuclei marker), and mounted in VectaShield reagent. Slides were imaged on an Innovative Imaging Innovations (3i) spinning disk confocal microscope equipped with a Yokogawa CSX-W1 using a 63X oil objective.

Staining: Astrocytes (red); Cortex glia (green); Neurons (blue)
description: Imaging mode: fluorescence microscopy
Visualization methods: Spinning Disk Confocal Imaging
description: Confocal image of the CNS of a D. melanogaster in the third instar larval stage after αSNAP KD, 6uM from the ventral surface, depicting astrocytes (red), cortex glia (green) and neuronal nuclei (blue). Our study examined the breakdown of the spatial segregation between cortex glia and astrocytes after disruption of cortex glial morphology. After knockdown of αSNAP, a protein part of the vesicual transport pathway, we observed aberrant infiltration by astrocytes into the cortex.
DOI: 10.6075/j0736pvd
title: CIL:34846, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: A high resolution tangential section through the buccal cavity showing the close spacing of the cilia in the undulating membrane and 3, presumably nonciliated basal bodies, in the inside row. Accessory microtubular ribbons arise from the basal bodies of the inner row and extend upward toward the oral ribs. Microtubular ribbons in the oral ribs are sectioned obliquely and alveolar segments lie between the ribbons. Portions of two membranelles are seen in the buccal cavity. TEM taken on 8/15/67 by R. Allen with Philips 200 operating at 60kV. Neg. 12,400X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis.
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
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/j0x34wzp
title: CIL: 51961, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

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
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.
DOI: 10.6075/j0tq60ds
title: CIL:32134, 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