cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j08w3cjr
title: CIL:1145, Caenorhabditis elegans, muscle cell. In Cell Image Library

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
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 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.
DOI: 10.6075/j0s75gd2
title: CIL:35829, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Cln1. Cln 1 is a cyclin-dependent protein kinase regulator. These phase and GFP images are part of an image group containing CIL 35820-35839. Note that there are additional groups of images of other cell cycle regulator proteins by the same authors available 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 read the microscopy section of the referenced paper for details before 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
DOI: 10.6075/j0222sqf
title: CIL:36640, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Standard glutaraldehyde fixation followed by osmium tetroxide, dehydrated in alcohol and embedded in an epoxy resin. Microtome sections prepared at approximately 75nm thickness. The negative was printed to paper and the image was scanned to Photoshop. This digitized image is available for qualitative analysis. 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; uranyl salt; lead salt; osmium tetroxide
Processing history: recorded image; film; Print from negative scanned for Photoshop.
Data qualification: Processed
description: Paramecium also contains many crystals in older cultures. This micrograph is of a crystal taken from a cell in stationary phase (day 8 post-inoculation). Crystals are enclosed by a membrane and contain sheets of paracrystalline material similar to that in lysosomes and phagolysosomes that lie just inside the membrane. The crystal membrane has a pronounced glycocalyx like phagolysosomes and lysosomes and may store digestive enzymes in a paracrystalline form during periods of starvation or limited food supply. TEM taken on 3/6/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 10,250X. Bar = 0.5µm.
DOI: 10.6075/j08s4nvf
title: CIL:32131, 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
DOI: 10.6075/j0833r6w
title: CIL:10428, Gallus gallus, erythrocyte. In Cell Image Library

description: Nucleated erythrocytes from chicken were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV using darkfield illumination. For this micrograph, the grid was tilted to 43 degrees. A similar micrograph tilted to 58 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image. The combination of shadowing and darkfield illumination gives a quasi-negative stain effect revealing nucleosomes in some fibers.
description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM); darkfield illumination
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0qf8rh9
title: CIL:45986, 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 26008 - Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.
 
Images
The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the .cell-painting. assay).
 
This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format.
DOI: 10.6075/j0sf2v1m
title: CIL:24800, Xenopus laevis, keratocyte. 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: Preparation: permeabilized tissue; glutaraldehyde fixed tissue
Relation to intact cell: dispersed cell 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; platinum replica
Processing history: unprocessed raw data
description: Structural differentiation of actin network in lamellipodium. Electron micrograph of Xenopus keratocyte after unprotected extraction without PEG and phalloidin. Actin network at lamellipodial rear disassembled in the course of unprotected extraction, whereas front zone remained as dense as in control cells (CIL 24801). Image corresponds to Figure 6b from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6075/j04m9367
title: CIL:39253, Mus musculus, myoblast. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; living tissue
Relation to intact cell: whole mounted tissue
Item type: photomultiplier tube (PMT); charge coupled device (CCD)
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: Fluorescein (FITC); EGFP
Processing history: montage
Data qualification: Processed
description: Mouse myoblast cells were engineered to express GFP-PCNA (proliferating cell nuclear antigen) as a marker for replication factories, and also immunostained for DNA ligase. DNA was localized using Hoechst staining. The image shows two different typical S-phase patterns displaying GFP-PCNA (left), DNA ligase (center) and DNA (right). DNA ligase co-localizes with PCNA at replication foci.
description: C2C12 cells stably expressing GFP-PCNA were fixed,stained for Dnmt1 and DNA, and optical sections acquired with a Leica TCS confocal microscope. 

See: Fig 2A in H Leonhardt et al. 2000 Dynamics of DNA replication factories in living cells. J Cell Biol 149:271-279
DOI: 10.6075/j0r210qr
title: CIL:1620, 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 0 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/j03b5xs6
title: CIL:30549, Homo sapiens, blood vessel endothelial cell, monocytic leukemia cell. In Cell Image Library

description: TNF-alpha stimulated p110alpha or control siRNA transfected HUVECs previously labelled with celltracker orange dye were grown on collagen matrices in transwell chambers. Celltracker green-labelled THP-1 cells were added to HUVECs, and TEM allowed to proceed toward an MCP-1 gradient in the lower chamber, for either 10 or 60 minutes before fixation. Fixed samples were stained with AlexaFluor 633-conjugated phalloidin to visualize F-actin (grey) and z-stacks collected. Three dimensional reconstructions were produced using Volocity software. A small gamma correction was applied to the red channel in order to visualise weak cell tracker staining at the edges of cell, which are difficult to distinguish upon 3D rendering. Transwells were fixed by immersion in 3.7% (wt/vol) paraformaldehyde before being processed for immunofluorescence microscopy. Images were acquired at room temperature using a confocal microscope (LSM 510 META; Carl Zeiss, Inc.) with three single photomultiplier tube confocal detectors mounted on an inverted microscope (AxioObserver Z1; Carl Zeiss, Inc.) at a magnification of 40 with an oil immersion objective (EC Plan-Neofluar 40× NA 1.30 oil differential interference contrast M27). z sections were acquired at 200-nm intervals by confocal microscopy. Corresponds to Figure 5 from J Cell Biol. 2010 Mar 22;188(6):863-76.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: intracellular filling; phalloidin; Alexa Fluor 633; CellTracker Green; CellTracker Orange
Processing history: 3D volume rendering; gamma correction
DOI: 10.6075/j0h131hq
title: CIL: 52161, Homo sapiens. In Cell Image Library

description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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 single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
DOI: 10.6075/j0vd6xzb
title: CIL: 52134, Homo sapiens. In Cell Image Library

description: Imaging mode: Fluoresence
Visualization methods: objective based TIRFM using a modified Nikon TE-2000U (60x 1.49 N.A. TIRF objective) and illumination from a 532-nm solid-state laser with power modification by neutral-density filters
description: A single molecule TIRFM assay was employed to measure the kinase activity of purified PI3K molecules on a supported lipid bilayer by counting the number of product PIP3 molecules they produce.
description: This assay utilizes physiological concentrations class I PI3Ka, 1mM ATP, drug identified in subfolder, and saturating concentrations of fluorescently-labeled GRP-PH domain, a PIP3 product lipid binder, in order to count each product lipid produced. Enzyme rates are calculated as the slope of product lipid created vs. time. 21.5 ± 0.5°C

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/j05h7g9n
title: CIL:35884, Saccharomyces cerevisiae. In Cell Image 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
description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP tagged Lte1. 
 
 LTE1 is essential for termination of M phase at low temperatures, along with TEM1, and CDC15, all part of the mitotic exit network which is an elaborate signaling system comprising at least eight essential genes: CDC5, CDC14, CDC15, DBF2, DBF20, LTE1, MOB1, and TEM1. LTE1 was originally discovered as a locus essential for growth at 8 C, and was named for this trait as Low Temperature Essential 1. It was later inferred from sequence similarities that LTE1 must code for a guanine nucleotide exchange factor. Genetic evidence suggests that Lte1p activates the GTPase Tem1p which activates the protein kinase Cdc15p. Cdc15p then relieves the inhibition of the protein phosphatase Cdc14p by Net1p, thereby allowing exit from mitosis. In a normal cell cycle, Bub2p bound to Tem1p restrains mitotic exit until the daughter-bound centrosome (with which both Bub2p and Tem1p preferentially associate) comes into contact with Lte1p in the bud, effectively coupling mitotic exit with nuclear segregation. Some evidence suggests that the spatial separation of Tem1p and Lte1p is a key mechanism for controlling the timing of mitotic exit.
 
 These phase,gfp images are part of an image group that ranges from CIL:35880-35899. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
DOI: 10.6075/j03f4psz
title: CIL:46754, Homo sapiens, mononuclear cytotrophoblast cell. In Cell Image Library

description: Many oval peroxisomes can be seen in normal cytotrophoblast cells of first trimester chorionic villus. The cytotrophoblast also contains glycogen particles, isolated and in flakes, which distinguish these cells from the syncytiotrophoblast (at left in this image). Bars = 1 µm (low magnification), 0.1 µm (high magnification). In some genetic diseases (Zellweger, Infantile Refsum) peroxisomes are absent; this can be diagnosed in chorionic villi.
description: Peroxisomes are contrasted with DAB at pH 10.5 by their catalase activity, after fixation in buffered formal-calcium; post-fixed in OSO4
description: Imaging mode: transmission electron microscopy (TEM)
DOI: 10.5281/zenodo.15050115
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