cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0wq03v6
title: CIL:36168, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
DOI: 10.57745/xywsce
title: 1_C_and_N_concentration.tab

description: soil organic carbon and total nitrogen concentration
DOI: 10.57745/t4dftr
title: 0_variable_list.tab

description: list and definition of the variables
DOI: 10.6075/j0125sd7
title: CIL: 54191, Homo sapiens, HeLa. In Cell Image Library

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
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: 10.57745/vwyueb
title: Dataset from a long-term experiment on the effect of cropping systems and tillage on soil organic carbon, total nitrogen, microbial biomass carbon and nitrogen mineralization rate

description: A long-term field experiment was conducted from 1989 to 2008 in Estrées-Mons, northern France. From 2000 to 2008, it compared three cropping systems (CS1, CS2 and CS3) varying in crop rotation or growth cycle duration and two tillage treatments: annual full inversion tillage (FIT) and shallow tillage (ST). Soil organic carbon, total nitrogen, bulk density, microbial biomass carbon and nitrogen mineralization rate were monitored during eight years in three soil layers (0-6, 6-20 and 20-30 cm). Half of the experimental plots were sampled every year according to the last ploughing year in ST, so that each plot was sampled every two years. Soil samples were collected in May or June in 2001-2002 (t = 1.5), 2003-2004 (t = 3.5), 2005-2006 (t = 5.5) and 2007-2008 (t = 7.5 years). This dataset includes data on: 1) soil organic carbon and total nitrogen concentration (average of four measurements per plot and layer); 2) soil bulk density, measured with a membrane densimeter for the first layer and with steel cylinders for the other layers (average of four measurements per plot and layer); 3) microbial biomass carbon concentration (one measurement per plot and layer); 4) mineralized nitrogen measured during soil incubation (168 days at 21 °C and a moisture content of 205 g kg-1); 5) nitrogen mineralization rate calculated from an exponential model fitted against the incubation data.
DOI: 10.6075/j08g8jqt
title: CIL:7421, Homo sapiens, neuron. In Cell Image Library

description: The protein MeCP2 binds to symmetrically methylated CpG dinucleotides and is thought to transmit the (generally) repressive signals encoded in DNA methylation patterns. Mutations in MeCP2 lead to Rett syndrome. Here, MeCP2-DNA complexes have been imaged by AFM (Digital Instruments Nanoscope) in air using human MeCP2 and an 828 bp DNA sequence containing several methylated CpGs. MeCP2, which appears as bright circles in AFM images, and volume measurements of the complexes suggest that MeCP2 monomers and dimers are present and that MeCP2 binds DNA cooperatively. Other images in the linked set show looped structures and large complexes containing multiple DNA strands and MeCP2 molecules. These configurations are likely promoted by the multiple independent DNA-binding domains of MeCP2.
description: Preparation: glutaraldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: microscopy; atomic force microscopy
Parameter imaged: specimen height
Source of contrast: specimen height
Processing history: Pixel value determine by specimen height
DOI: 10.6075/j02b8x89
title: CIL:2179, Caenorhabditis elegans. In Cell Image Library

description: Terminal Bulb is a dataset of DIC (differential interference contrast) 20x microscopy images of the pharynx terminal bulb of C. elegans at different ages (0, 2, 4, 6, 8, 10, 12 days). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1587, 1694, 1905, 2213, 2622, 2544, and 2606, respectively.
description: The purpose of the dataset C. elegans terminal bulb aging is to deduce the age of the nemathode based on images of the pharynx terminal bulb (part of the eating apparatus). Images of C. elegans were taken at different chronological ages. This image is part of the day 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: 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/j0q81c6b
title: CIL:24566, Balamuthia mandrillaris, cell by organism, eukaryotic cell, Eukaryotic Protist, Amoeboid Protist. In Cell Image Library

description: A frame from the grouped movie of a Balamuthia mandrillaris ameba within a culture of monkey kidney cells. Accompanying photographs are enlargements of the tips of pseudopodia to demonstrate their flexibility and movement, and a second set of photographs demonstrate the puncture of the plasma membrane of a monkey kidney cell. The first shows an indentation in the cell membrane, the withdrawal of the pseudopodia tip and the subsequent rupture of the membrane in the area indented by the amebic tip. The eventual break in the membrane may have resulted from the release of a proteolytic enzyme. Details of the preparation can be found in CIL:19325.
description: Preparation: living tissue
Relation to intact cell: living tissue; whole mounted tissue
Item type: microscopy; in-focus phase contrast
Imaging mode: retardance; phase contrast microscopy
Parameter imaged: boundaries between regions with different refractive index
Source of contrast: boundaries between regions with different refractive index
Visualization methods: natural boundaries
Processing history: living tissue; recorded image; charge coupled device (CCD)
Data qualification: Raw
DOI: 10.6075/j0bv7gn4
title: CIL:36174, Rattus, multipolar neuron. In Cell Image Library

description: Synapse development in cultured hippocampal neurons after 15 days in vitro. Neurons were immunostained for MAP2, a microtubule associated protein localized to dendrites (green) and the presynaptic vesicle protein Synapsin I (red) to show the density of presynaptic contacts along the dendritic arbor.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (monoclonal HM2, Sigma, with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and synapsin I (from P. DeCamilli, with DyLight549 conjugated secondary, excitation, 555, emission, 568, [Jackson Immunoresearch]). Images were acquired with a Leica DMRA microscope with a 20X objective (Fluotar, 0.5NA), Photometrics CoolSnap ES CCD camera and MetaMorph software. This color was generated using the MetaMorph "color combine" function.
DOI: 10.6075/j0t43s9z
title: CIL:12371, Nephrotoma, Nephrotoma suturalis, primary spermatocyte. In Cell Image Library

description: Movie showing the dynamics of kinetchore microtubules during meiosis I in primary spermatocytes of the crane-fly Nephrotoma suturalis that were experimentally flattened. Time-lapse polarization microscopy using a Nikon Microphot SA, equipped for liquid crystal polarized light microscopy 
(LC-PolScope, CRi, Woburn Massachusetts) 60x/1.4 PlanApo oil immersion objective, 1.4 NA oil imm. condenser, with 2.0x zoom lens. Images captured every 15 sec using a QImaging Retigo EXi CCD camera. Raw images were processed 
using 5-frame algorithm (Shribak and Oldenbourg, 2003). The time series used to make the movie is included in this grouped set.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: charge coupled device (CCD); Processed image based on 5 recorded images
Imaging mode: polarization microscopy
Parameter imaged: UV/visible/IR photons
Source of contrast: intrinsic birefringence
Visualization methods: relative retardation (retardance) measurement
Processing history: 5-frame algorithm
DOI: 10.6075/j0736q3z
title: CIL:21727, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Quick-freeze deep-etch of the P-face of the contractile vacuole. This face has many IMPs that are presumably transmembrane proteins many of which have been pulled free of the leaflet. There are also pits in this leaflet which represent the IMPs that remain with the opposite leaflet. Although we have found no mechano-sensitive or voltage-gated channels in the CVC (Sugino et al., J. Exp. Biol. 208:3957-3969, 2005) it is clear that proton pumps are present in the decorated tubules and that protons are exchanged for other ions such as calcium, potassium and sodium as these ions can accumulate in the CV against a concentration gradient from the cytosol. Some of the IMPs may function as ion exchange channels. What caused the large holes is not known. The texture of the luminal contents resembles the CV content and indicates the membrane is indeed that of the contractile vacuole. TEM taken on 5/27/92 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. Bar = 0.2µm. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:13128) is available for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: shadowing and plating; freeze_fracture/freeze_etch; isolated subcellular component
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: electron density
Parameter imaged: elastic scattering of electrons; electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: transmission electron microscopy (TEM)
Processing history: freeze_fracture/freeze_etch; shadowing and plating; recorded image; film; Print of negative scanned for Photoshop
Data qualification: Processed
DOI: 10.6075/j0dn43n0
title: CIL:27850. 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/j0db81j7
title: CIL: 53979. In Cell Image Library

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.
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/j0dn43t7
title: CIL:40317, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: Transmission electron micrograph of a thin section of the nucleus of a normal HeLa cell showing a tangential view of the nuclear envelope with nuclear pores. From a study of the role of the nuclear porin ALADIN. Other images in this group show additional details of nuclear pore structure.
description: Preparation: glutaraldehyde fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-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
Visualization methods: osmium tetroxide; uranyl salt; lead salt
Data qualification: Processed
description: Normal HeLa cells expressing were fixed with glutaraldehyde, embedded in epoxy resin, thin sectioned, and imaged using a Philips CM10 TEM.
See: J Cronshaw and M Matunis 2003 The nuclear pore complex ALADIN is mislocalized in triple A syndrome Proc Natl Acad Sci USA 100 5823-5827
DOI: 10.6075/j01835n7
title: CIL:13134, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: The cytoproct ridge at higher magnification. The unique system of thick fibers extends from each side of the ridge toward the center of the ridge. These thickened fibers are not found in any other part of the cell's surface. Also extending from the ridge tip are single microtubules that extend down into the cytosol. These microtubules may make contact with the surface of the approaching vacuole's membrane and help to pull the vacuole membrane and the plasma membrane together to promote their fusion. The role of the thickened fibers is unclear, they may cross link to prevent the cytoproct from an untimely opening under stress. A few vesicles get trapped in the ridge. TEM taken on 6/1/84 by R. Allen with Zeiss 10A 80kV. Neg. 19,800X. Bar = 0.2µm. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. An unprocessed, high resolution version of this image (CIL:12349) is in the library and available for quantitative analysis. Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment; microtome-sectioned tissue
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM); illumination by electrons
Imaging mode: detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: stain with broad specificity; osmium tetroxide; uranyl salt; lead salt
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
DOI: 10.6075/j0dz0789
title: CIL:35619, Homo sapiens, keratinocyte. In Cell Image Library

description: Preparation: chemically fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Alexa Fluor 488; phalloidin
Processing history: unprocessed raw data
description: Image collected on a Zeiss Axiovert 200M microscope using a 63X 1.4 NA objective. Image was contrast stretched using Image J.
description: Actin fiber organization in primary keratinocyte. There are numerous actin arcs around the periphery of the cell and actin bundles that terminate in focal adhesions (bright structures perpendicular to edge).
DOI: 10.6075/j0c24wb9
title: CIL: 54828, Alysiella filiformis, bacteria. In Cell Image Library

description: Imaging mode: confocal microscopy
Visualization methods: fluorescent d amino acids
description: Leica TCS SP8 X; 63X Plan-Apochromat glycerine objective with a NA of 1.30 and a refraction index of 1.46.
description: Screnshot showing the position of a synthesized septum within the A. filiformis filament.
DOI: 10.6075/j0n58ksf
title: CIL: 50972, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: populations of ~1200 cells plated on glass in standard media were imaged at 37º C in each experiment. A target subpopulation of ~100 cells display a readily observed extended, ruffling leading edge pseudopod . The cells exhibiting these deployed, extended pseudopods were counted in each unit area at 6 timepoints during the 3 hr observation period following rapid addition of drug to its standard working concentration. Altogether, 6 experiments were carried out for each treatment, yielding average timecourses summarizing observations of ~600 polarized cells.

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 a full therapeutic dose at once at t=0.
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/j09k4b2n
title: CIL: 54742, Homo sapiens, SBAD2 human iPSC line. In Cell Image Library

description: Imaging mode: confocal laser scanning microscopy
Visualization methods: confocal fluorescence imaging
description: iRFP720 expressing cells.
description: Live cell fluorescent imaging.