cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0sj1kw5
title: CIL:56174, Homo sapiens. In Cell Image Library

description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Scan 10_F_TI_C -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
DOI: 10.6075/j0fj2h2v
title: CIL:55882, Homo sapiens. In Cell Image Library

description: Scan 03_E_CD_D -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
DOI: 10.6075/j0dn45c7
title: CIL:56365, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scan 22_B_DD_C -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
DOI: 10.6075/j0g16152
title: CIL:56137, Homo sapiens. In Cell Image Library

description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scan 09_I_CS_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
DOI: 10.6075/j07944x0
title: CIL:55528, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Scan 13_H_CD_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
DOI: 10.6075/j0nv9j1f
title: CIL: 54401, Drosophila melanogaster, Entire Organism. In Cell Image Library

description: Imaging mode: Gray Scale
Visualization methods: 20x magnification captured by one of the following eyepiece cameras: Swiftcam 3 Megapixel, OMAX 9.0 MP, AmScope MU300
description: 14.3 degrees ℃
description: Video of fruit fly embryonic development. Video filename format is as follows organism_temperature_embryo. Data was collected at 14.3 degrees Celcius
DOI: 10.6075/j0v40tpg
title: CIL: 51975, Mus musculus, RAW 264.7 TIB-71. In Cell Image Library

description: ~1200 cells were imaged on glass. More gradual additions of drug or carrier were carried out in four equal increments at 0, 30, 60, 90 min, together yielding the same final drug concentration indicated in rapid addition studies. The subpopulation of ~100 cells with extended, leading edge pseudopods at t = 0 were imaged and counted in each unit area at the indicated timepoints during a 125 min observation period T=37C

Images are provided as uncorrected, 16 bit .nd2 files to preserve all original data. To view these .nd2 files:
1. Download ImageJ viewer at (https://imagej.nih.gov/ij/download.html)
2. Download the BioFormats.jar package at (https://www.openmicroscopy.org/bio-formats/downloads/)
3. Open the ImageJ directory after installation and drag the extracted BioFormats.jar package into the "Plugins" subdirectory
4. Open an .nd2 image using imageJ and select opening options when prompted, if desired. If no modifications are desired, select "OK"
5. The 16 bit image will typically look dark and will require brightness adjustment.
6. In the ImageJ toolbar, select Image &gt;&gt; Adjust &gt;&gt; Brightness/Contrast and select "Auto", or manually set the brightness and contrast.
description: 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: 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/j0j9667d
title: CIL:36987, Xenopus laevis, CNS neuron (sensu Vertebrata). In Cell Image Library

description: This is IMAGE #4 (30 minutes) of a time lapse series contained with in this image group. It shows a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47.
 
 The images were acquired with 10 minute intervals and show morphological plasticity of the dendritic arbor with branch additions and retractions.
 
 The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope.
 
 Images were acquired every 10 minutes for 1 hour. After 60 minutes, the animal was placed in a 50 microMolar anisomycin solution for ~1.5 hours. A second time lapse series (10 minute interval for 60 minutes) was then acquired.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: multi-photon microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: 
Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. 

The methods of cell transfection with electroporation can be found here: 
Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. 

Further explanation can be found here:
Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499.

Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10.
DOI: 10.6075/j09022q7
title: CIL:34532, Tetrahymena pyriformis, 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. 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; unprocessed raw data
Data qualification: Raw;spatialmeasurements
description: High resolution image of the cytoplasm of Tetrahymena. Mitochondria have tubular cristae, infoldings of their inner membranes. Peroxisomes, with a few tubular inclusions, mucocysts, and a planar view of rough ER, to which many polysomal ribosome arrays are attached, fill the cytosol. TEM taken on 2/11/71 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 19,500X. The raw film was scanned with an Epson Perfection V750 Pro. This image is best used for quantitative analysis.
DOI: 10.6075/j0hx1brs
title: CIL:7122, Homo sapiens, neuron. In Cell Image Library

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: unprocessed raw data
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 molecules appear as bright particles in AFM images. Volume measurements of the complexes suggest that MeCP2 monomers (circular particles) and dimers (larger elliptical particles) are present and suggest that MeCP2 binds DNA cooperatively. Other images in the grouped 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 and relevant to the in vivo interactions between MeCP2 and chromatin.
DOI: 10.6075/j0862fx7
title: CIL: 52218, Homo sapiens. In Cell Image Library

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
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/j0dn43w4
title: CIL:50623, Homo sapiens, monocyte. In Cell Image Library

description: One omoncyte contained 2 erythrocytes. To note would be the presence of lytic material with erythrocyte-type aspect at contact to the monocyte surface.
description: Cerebrospinal fluid, cytocentrifugation, May-Grunwald-Giemsa stain.
description: Imaging mode: microscopy
Visualization methods: x100
DOI: 10.6075/j0dv1jb8
title: CIL: 51808, 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/j0td9xff
title: CIL:39608, Saccharomyces cerevisiae. In Cell Image Library

description: Images were collected at 4-minute intervals on a DeltaVision system equipped with a with a 60x PlanApo
PH3 phase-contrast, oil immersion objective (NA = 1.4). This system has a motorized x-y-z stage, automatic focusing, motorized illumination shutters and a CoolSNAP_HQ2 camera.
description: 10-hour timelapse of Wild-type Saccharomyces cerevisiae growing in 2% raffinose. These experiments are the control experiments used for comparison to the effects of the double mutant Clb2dbŒî, Clb5Œî on the cell cycle control system in budding yeast. The images from two experiments done with Wild-type Saccharomyces cerevisiae are available as CIL:39606-39625 and CIL:39646-39665. The images from two experiments done with the double mutant Clb2dbŒî, Clb5Œî are available as CIL:39626-39645 and CIL:39666-39685.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: phase contrast microscopy
Parameter imaged: elastic scattering of photons
Source of contrast: differences in amount of elastic light scattering
Visualization methods: visualization of contiguous regions
Processing history: unprocessed raw data
DOI: 10.6075/j0xk8fsd
title: CIL:55441, Homo sapiens. In Cell Image Library

description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scan 11_C_ED_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
DOI: 10.6075/j0h1329f
title: CIL:56199, Homo sapiens. In Cell Image Library

description: Scan 10_J_CD_E -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
DOI: 10.6075/j09w0frf
title: CIL:56141, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scan 09_I_CS_F -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
DOI: 10.6075/j0pk0gc7
title: CIL:55552, Homo sapiens. In Cell Image Library

description: Scan 14_D_EP_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.
description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
DOI: 10.6075/j0h70g26
title: CIL:55483, Homo sapiens. In Cell Image Library

description: Imaging mode: Static digital pathology tissue scans
Visualization methods: Hematoxylin and eosin
description: Scan 11_K_RE_B -- The dataset consists of 951 tissue section scans taken from 167 H&E-stained whole slides from 18 pediatric inflammatory bowel disease (IBD) patients. Slide section scans are provided as-is without any initial image pre-processing, normalization, or cropping. Labels are provided at the patient, slide (anatomic site), and section (tissue slice) levels. Each slide is labelled with biopsy site and normal or abnormal classification per the surgical pathology report. Each tissue section scan from an abnormal slide is further classified as normal or abnormal by pathologist. Files may be viewed and annotated using standard, opensource slide-viewing software, such as Aperio ImageScope, OpenSlide​​, TiffSlide, and QuPath​​.
description: Scans of H&E-stained histology slides of biopsied tissue from endoscopy. Captured with MikroScan SL5 in SVS TIFF format with .tif file extension.