cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17490357
title: Debris Flow Hazard-Causing Factors Dataset for the Yunnan Section of the Nujiang River Basin, China

description: This dataset contains hazard-causing factors for debris flow prediction using deep learning models. The data were collected from the Yunnan Section of the Nujiang River Basin, China, a region characterized by complex geological conditions and high debris flow susceptibility. The dataset encompasses topographical, hydrological, geological, meteorological, and vegetation-related factors derived from multi-source data integration, including SRTM DEM (30m resolution), meteorological station observations, and field investigations.

The dataset comprises 159 debris flow-prone gullies with 15 influencing factors systematically selected through multicollinearity diagnosis. Four variables (X10, X14, X17, X19) were excluded from the original 19 candidate factors due to multicollinearity (Variance Inflation Factor > 5.0) to ensure model stability and parameter precision. The variable numbering is preserved for consistency with the research methodology.

    


Variable Code
Description
Unit
Data Type


No
Sample ID
-
Integer


X1
Maximum 24-hour Rainfall
mm
Float


X2
Annual Average Rainfall
10³mm
Float


X3
Annual Average Temperature
°C
Float


X4
Annual Average Wind Speed
m/s
Float


X5
Annual Average Vapor Pressure
hPa
Float


X6
Annual Average Relative Humidity
%
Float


X7
Potential Source Energy
10⁹ J/m²
Float


X8
Catchment Area
km²
Float


X9
Average Gradient of Main Channel
-
Float


X11
Length of Main Channel
km
Float


X12
Sinuosity of Main Channel
-
Float


X13
Drainage Density
km/km²
Float


X15
Vegetation Cover Rate
%
Float


X16
Average Slope
°
Float


X18
Lithological Impact
-
Float
DOI: 10.6075/j08c9tx5
title: CIL:34916. In Cell Image Library

description: Procedures for detergent extraction, immunostaining, S1 decoration, light, and EM were described previously (Svitkina et al., 1995, 1996, 1997;Verkhovsky et al., 1995; Svitkina and Borisy, 1998).
description: Localization of Arp2/3 complex at actin filament branching points. Xenopus keratocytes and fibroblasts were treated with CD (0.2 μM for 30 min or 0.5 μM for 10 min), extracted in the presence of phalloidin, fixed with glutaraldehyde, treated with 33% methanol, and immunostained with p21 antibody followed by 10-nm gold-conjugated secondary antibody. Image corresponds to a single panel from Figure 4 in J Cell Biol. 1999 May 31;145(5):1009-26. All of the panels from Figure 4 are available as CIL:34902-34921.
description: Preparation: permeabilized tissue; glutaraldehyde fixed tissue; methanol fixed tissue; phalloidin
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM)
Parameter imaged: optical path length gradient
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating; primary antibody plus labeled secondary antibody; platinum replica; immuno-gold
Processing history: unprocessed raw data
DOI: 10.6075/j0000170
title: CIL:12083, Paramecium tetraurelia, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Cells were lightly fixed with 0.25% glutaraldehyde and infiltrated with 2.3M sucrose before being frozen in liquid nitrogen and thin sectioned at a temperature of –100°C at approximately 75nm thickness. Frozen sections from these preparations were then thawed, washed, and exposed to a monoclonal primary antibody that was raised in mice or rabbit/goat and to colloidal gold-complexed goat-anti-mouse/rabbit secondary antibodies. Further details of preparation are detailed in Methods Cell Biol. 2010;96:143-73. The raw film was scanned with a Nikon Coolscan 9000ED. This image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: A high resolution view of the radial arm of the Contractile Vacuole Complex or CVC each contain a collecting canal enclosed by a microtubular ribbon split lengthwise into several smaller ribbons, a meshwork of smooth spongiome and, peripheral to this, the bundles of tubules of the decorated spongiome. The microtubules along the collecting canal are immunogold-labeled with anti-b-tubulin as are some single microtubules in the area. TEM taken on 7/8/96 by R. Allen with Zeiss 10A operating at 80kV. Neg. 7,900X.
description: Preparation: glutaraldehyde fixed tissue; tissue in vitreous ice embedment; microtome-sectioned tissue; monoclonal antibody
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: intrinsic mass distribution; stain with broad specificity
Visualization methods: stain with broad specificity; uranyl salt; gold
Processing history: recorded image; film; unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j04f1qt0
title: CIL:39567, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged ESP1. ESP1 is essential for dissolving the cohesins that hold the sister chromatids together. ESP1 activation results in proper separation of sister chromatids at anaphase ESP1 also inhibits protein phosphatase 2A-Cdc55p to promote mitotic exit.These phase,gfp z-series images are part of an image group that ranges from CIL:39566-39570. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. 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
DOI: 10.6075/j0tb15g2
title: CIL:46276, Homo sapiens. In Cell Image Library

description: Plate 25694 - 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/j03j3bvc
title: CIL:35388, Drosophila melanogaster, salivary gland. In Cell Image Library

description: Preparation: chemically fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment; paraformaldehyde fixation
Relation to intact cell: microtome-sectioned tissue
Item type: film
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt
Processing history: unprocessed raw data
description: High Voltage (1MeV) TEM image of a 'thick' section of polytene chromosome from salivary gland of 3rd instar larva of Drosophila melanogaster showing the band-interband organization. This image was captured with a specimen tilt of 56 degrees. Grouped with it is an image of the same region taken at a tilt angle of 45 degrees, providing an oblique stereo view of the structure.
description: Salivary glands were dissected, fixed with paraformaldehyde, post-fixed with osmium tetroxide, and embedded in plastic. 4 micron sections were cut, stained with aqueous uranyl magnesium acetate, and observed with the Wisconsin HVEM at 1 MeV. See Ris, H 1981 Stereoscopic Electron Microscopy of chromosomes. Meth Cell Biol 22:77-96; Ris, H 1978 Preparation of chromatin and chromosomes for electron microscopy. Meth Cell Biol 18:229-246
DOI: 10.6075/j0h70ddv
title: CIL:49180, Homo sapiens. In Cell Image Library

description: Plate 24514 - 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. 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 experiment consists of 375 plates in 384-well format, for a data set comprised of 988,994 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 approximately 5 million 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 375 microtiter plates. Each plate has 384 wells. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale 16-bit TIFF image file.

The experiment consists of 375 microtiter plates. Each plate has 384 wells. 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/j06w99f7
title: CIL:39798, Tetrahymena pyriformis, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: During division new basal bodies develop accessory fibers and begin to move apart to take up a position equidistant between the older complexes. The new kinetodesmal fiber seems to be associated with the prexisting kinetodesmal fiber during separation. TEM taken on 8/15/67 by R. Allen with Philips 200 operating at 60kV. Neg. 12,400X. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
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/).
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/j0mk6c2m
title: CIL:9902, Euplotes sp., cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: An image showing the mitochondria packed with tubular cristae and the cytosol contains a jumble of microtubules. Basal bodies of the somatic kineties appear as dikinetids with a ribbon of transverse microtubules arising from the anterior basal body. The cytosol near the basal bodies is filled with ribosomes while dense rosettes of glycogen are found at the level of the mitochondria. TEM taken on 8/3/67 by R. Allen with Philips 200 operating at 60kV. Neg. 19,200X. Bar = 0.2µm. A print of the negative was scanned and processed in Photoshop. This image is best used for qualitative analysis. A high resolution image (CIL:9703) is 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. Additional information is available at (http://www5.pbrc.hawaii.edu/allen/).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in epoxy resin embedment
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;spatialmeasurements
DOI: 10.6075/j0wd3zbv
title: CIL:40566, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Preparation: glutaraldehyde 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; uranyl salt
Processing history: recorded image; film
Data qualification: Raw;spatialmeasurements
description: Glutaraldehyde fixation followed by Gomori staining, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The raw negative was scanned with an Epson Perfection V750 Pro and this high resolution image is best used for quantitative analysis. Additional information available at (http://www5.pbrc.hawaii.edu/allen/).
description: Acid phosphatase is present in tubules retrieved from late DV-III. The tubules and rounded expansions arising as a result of late DV-III membrane retrieval contain an electron-opaque reaction product when the cells are incubated in Gomori‚Äôs reagent and lead salts. This indicates that acid phosphatase (AcPase) is being retrieved from the late phagolysosomes before the spent vacuole contents are released at the cytoproct. In fact, spent vacuoles no longer contain active AcPase and are free of AcPase-reaction product before they are defecated. (For details of lysosome recycling see Allen and Fok, J. Cell Biol. 99:1955-1959, 1984). TEM taken on 4/27/84 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Part published in J. Cell Biol. 99:1955-1959, 1984. Adapted with permission.
DOI: 10.6075/j03r0smj
title: CIL: 54021, 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: 10.6075/j0g160vm
title: CIL:10226, Rattus, multipolar neuron. In Cell Image Library

description: This multi-layer image shows the spatial relationship between filamentous actin (red) and microtubule array (green) in cultured hippocampal neurons, grown for 3 days in vitro. Actin staining (with rhodamine phalloidin) highlights the growing tips and filopodial extensions along axons and dendrites, while microtubule staining reveals the stable shafts of these processes. Some nonneuronal cells may also appear in the field. Neurons at 1, 3 and 5 days in vitro are represented in this image group.

Detailed Methods: 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, 37°C, 15 minutes), permeabilized (0.25% Triton, 7 minutes) and immunostained for tubulin (monoclonal DM1A, Sigma, with Alexa 488 conjugated secondary, Molecular Probes, excitation, 494, emission, 519) and rhodamine-conjugated phalloidin (Molecular Probes, excitation, 540, emission, 565). Fluorescent and phase images were acquired with a Leica DMRA microscope with a mercury arc lamp, a 40X lens (HCX PL Fluotar, NA 0.75), Leica GFP filter set (excitation, BP 470/40; dichromatic mirror, 500, suppression filter, BP 525/50); Leica N3 filter set (excitation, BP546/12; dichromatic mirror, 565, suppression filter, BP 600/40), Photometrics CoolSnap ES CCD camera and MetaMorph software.
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; differences in adsorption or binding of stain
Visualization methods: phalloidin; primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
DOI: 10.6075/j02806r5
title: CIL:14687, Oscillatoria tenuis. In Cell Image Library

description: Preparation: freeze_fracture/freeze_etch
Relation to intact cell: whole mounted tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM)
Source of contrast: electron density
Visualization methods: shadowing and plating
Data qualification: Raw;spatialmeasurements
description: The thylakoids of the vegetative cells of the filamentous cyanobacteria, Oscillatoria tenuis, are capable of oxygen-evolving photosynthesis. Freeze-fracture replicas of the vegetative cells revealed the structure of the thylakoids. 

The process of freeze-fracture splits memebranes along their hydrophobic interior revealing two complementary fracture faces.

Oscillatoria cultures were maintained on agar plates. Cells were collected and suspended in 10 mL dH2O, spun at 2,000 g for 10 min in a clinical centrifuge, resuspended in 5 mL dH2O. Added 5 mL 70% glycerol over 1 hr with continuous stirring, spun at 2,000 g for 10 min in a clinical centrifuge. Pellets were placed on copper support discs, frozen in liquid Freon 12 and stored under liquid nitrogen. Replicas were prepared on a Blazers BA 360 freeze-etch unit and examined in a JEOL TEM 100C at 16,000X magnification.