cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0mw2fvb
title: CIL:13657, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: HeLa cells transiently expressing GlcNAcT-1-HA-KDEL were fixed, immunolabeled for GlcNAcT-1-HA-KDEL (red) and endogenous alpha-mannosidase II (ManII, green), and examined by fluorescence microscopy. Endogenous ManII displayed different staining patterns, depending upon the level of expression of GlcNAcT-1-HA-KDEL. In this image, GlcNAcT-1-HA-KDEL was highly expressed and ManII protein was lost, presumably due to ER degradation. Other images in Fig 6 show ManII localization to the Golgi (CIL# 13656), or to the ER (CIL# 13655). Transfected HeLa cells were fixed in 3% paraformaldehyde, blocked with 0.2% Triton X-100, 1% FBS, 0.5% BSA in PBS with Ca[2+] and Mg[2+], followed by incubation in primary antibodies (anti–human ManII rabbit pAb and anti-HA mouse mAb, HA.11 (Covance)) and secondary antibodies (Alexa 568 and Alexa 488) and DAPI (blue) to stain nuclei. Cells were mounted using Fluoromount (SouthernBiotech). Immunofluorescent images were digitally acquired on an inverted microscope (Axiovert 200M; Carl Zeiss, Inc.) coupled to a 12-bit cooled charge-coupled device camera (AxioCam MRm Rev. 3; Carl Zeiss, Inc.) controlled by Axiovision software (AxioVs40, version 4.7.2.0; Carl Zeiss, Inc.), using a 100x/1.3 NA oil immersion objective (EC Plan-NeoFluar; Carl Zeiss, Inc.), and saved as tiff files (1388 × 1040, 8 bit). All pictures were treated identically using Adobe Photoshop to remove background and adjust contrast. This image corresponds to Figure 6D, bottom panel (merge) in J Cell Biol. 190: 893-910, 2010. Images in Fig 6 include CIL#s 13655, 13656, 13657.
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 a specific protein; compartmentalization of stain or label
Visualization methods: Alexa Fluor 488; Alexa Fluor 568; 4',6-diamidino-2-phenylindole (DAPI); primary antibody plus labeled secondary antibody; HA peptide tag
Data qualification: Processed;spatialmeasurements
DOI: 10.6075/j04j0cq5
title: CIL:46260, Homo sapiens. In Cell Image Library

description: Plate 26623 - 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/j0xg9pt3
title: CIL:13555, Homo sapiens, epithelial cell, cervical carcinoma. In Cell Image Library

description: GalNac-T1 (green) and ERGIC53 (ER-to-Golgi intermediate compartment) (red) colocalize in unstimulated HeLa cells moderately only at the Golgi apparatus. Helix Pomatia Lectin (HPL) (gray) staining is included. HPL binds various glycans but the Tn antigen in particular. The Tn antigen refers to terminal α-linked N-acetyl galactosamine residues (GalNAc) linked to Ser or Thr residues. HeLa cells were serum starved overnight in DME (noFBS). Cells were fixed for 10 min (4% paraformaldehyde) and permeabilized (0.2% Triton X-100). Primary antibody staining followed the manufacturer's instructions. Cells were subsequently stained for 15–30 min with secondary Alexa Fluor–conjugated antibodies (Alexa 488 for anti-GalNac-T1, Alexa 594 for ERGIC53). Hoechst (blue) and Alexa 647-conjugated-HPL were added during secondary antibody incubations. Cells were mounted onto glass slides using FluorSave (Merck) and imaged at room temperature using an inverted FluoView confocal microscope (model IX81; Olympus) with fluorescence excitation at 488 nm, 543 nm and 633 nm and either a 60x objective (U Plan Super Apochromatic [UPLSAPO]; NA 1.35) or 100x objective (UPLSAPO; NA 1.40) using Immersol oil. Microscope coupled with a CCD camera (model FVII). Images were acquired and processed using Olympus FV10-ASW software. Image corresponds to Fig 4A in J Cell Biol. 189: 843-858. 2010. Images in Fig 4 include CIL#s 13555, 13556, 13557, 13558.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein; distribution of epitope; compartmentalization of stain or label
Visualization methods: Alexa Fluor 647; Alexa Fluor 594; Alexa Fluor 488; primary antibody plus labeled secondary antibody; Helix pomatia agglutinin; Hoechst
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0bp01g4
title: CIL:13478, Drosophila melanogaster, garland cell. In Cell Image Library

description: Ema localizes to endosomes. Third instar larval garland cells expressing Ema-GFP fusion protein and stained for the early endosomal protein Rab5 (red) and plasma membrane and nuclei (blue). Ema does not co-localize with early endosomes. Wandering third instar larvae were dissected in ice-cold PBS, equilibrated in HL-3 buffer at room temperature, incubated in 0.7% HRP for 5 min at room temperature, rinsed thoroughly and fixed in 4% paraformaldehyde in PBS for 30 min. Blocking and antibody incubation were performed in PBS containing 0.1% Triton X-100. Anti-Rab5 (Wucherpfennig et al., 2003) at 1:50. NeuroTrace 640/660 deep red fluorescent Nissl (Invitrogen) used at 1:500 was used to stain nuclei. Cy5-conjugated anti-HRP (Jackson Immunoresearch Laboratories) at 1:1000 was used to stain plasma membrane. Cy3-conjugated secondary antibody (Jackson Immunoresearch Laboratories, Inc.) at 1:1,000. Confocal images were acquired with a confocal microscope (model C1; Nikon) and accompanying EZ-C1 software using argon (excitation at 488 nm) and HeNe (excitation at 543 and 633 nm) lasers and a 60x Plan-Apochromat NA 1.4 objective (Nikon) at room temperature. Samples for each experiment were processed using the same confocal gain setting. Image corresponds to Fig 3C in Kim et al. J Cell Biol. 188: 717-734. 2010.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: whole mounted tissue
Item type: recorded image; photomultiplier tube (PMT)
Imaging mode: fluorescence microscopy; confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein; distribution of a specific nucleic acid sequence; distribution of epitope
Visualization methods: EGFP; Cy5; Cy3; Deep-red fluorescent Nissl stain
Data qualification: Raw
DOI: 10.6075/j0fj2fqj
title: CIL:36663, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: In one experiment in which electric shock was applied to Paramecium cells to trigger trichocyst discharge the macronucleus in one cell was observed to undergo morphological changes of two types. First, a large area of the nucleus, normally found to contain electron-opaque foci, had changed into whorls of more electron-transparent filamentous material. Secondly, a section of the nuclear envelope had folded into a stack like the annulate lamellae seen in oocytes of many vertebrate and invertebrate cells (see Kessel, Int. Rev. Cytol. 82:181-303, 1983). The nuclear pores were present in part of this stack of the nuclear envelope while in other parts the pores were reduced or absent and a layer of dots or lines occupied the nucleoplasmic space between the two envelope segments. Presumably these annulate lamellae represent a temporary storage mechanism for excess nuclear envelope. TEM taken on 2/28/84 by R. Allen with Zeiss 10A operating at 80kV. Neg. 12,000X. Bar = 0.5µm.
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/).
DOI: 10.6075/j0sq8z9g
title: CIL:36662, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: In a 9-day old culture of stationary phase cells, two or three days post-conjugation, remnants of the previous macronucleus could be found near normal macronuclear bodies. This remnant was identified by its nuclear envelope and a nucleolar body. A sparsely dispersed array of other electron-opaque bodies was present but these were far fewer than in a normal macronucleus. Presumably this body represents a breakdown product of the disintegrating macronucleus that was present before the preceding conjugation that occurred on day 6 or 7. TEM taken on 3/6/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 3,500X. Bar = 1µm.
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: 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/).
DOI: 10.6075/j0765db1
title: CIL:36660, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: An extreme example of peeling of the surface of nucleoli in which long threads unravel from the nucleoli. TEM taken on 5/27/82 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 14,250X. Bar = 0.25µm.
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/).
DOI: 10.6075/j0qv3kg1
title: CIL:36671, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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: In this micrograph of a developing organelle, the trichocyst membrane is intact but does not bear the glycocalyx seen on the luminal side of the lysosomal membrane that lies nearby. The flocculant material shows no sign of crystallizing. An electron transparent zone has formed around the inside of the membrane of the largest vesicle. This cell was taken from day 2 of a culture age study. TEM taken on 3/28/80 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 18,000X. Bar = 0.2µm.
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/).
DOI: 10.6075/j0251h45
title: CIL:36679, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Tangential fractures through mature trichocysts. The planes in the paracrystalline stacks are exposed. The body is laced to the membrane but such associations must be severed when the trichocyst is discharged as the membrane remains in the cell and is not extruded. Pits are present on the E-face of the membrane. TEM taken on 6/27/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 15,900X. Bar = 0.5µm.
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/j0m04497
title: CIL:36669, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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
description: A favorable view of one trichocyst docking site in a quick-freeze deep-etch image shows the prominent outer ring of 37 IMPs and about the same number of IMPs in the inner ring more deeply embedded in the cytosolic leaflet. Pits, where the rosette was removed during fracturing of the chemically-unfixed rapid-frozen cell, are seen at the center of the docking site. Two gaps in the rings indicate the site of the septum in the underlying alveoli where the plasma membrane is not linked to the alveolar rims by the ring IMPs. TEM taken on 2/15/90 by R. Allen with Zeiss 10A operating at 80kV. Neg. 31,500X. Bar = 0.2µm.
DOI: 10.6075/j06q1w5x
title: CIL:36668, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: In quick-freeze deep-etch preparations in which cells are slam frozen the pellicle and the plasma membrane tends to be flattened. The double rings are present but only the outer ring of IMPs stand out prominently. The inside ring seems embedded more deeply into the plasma membrane‚Äôs P-face, i.e., into the cytosolic leaflet of this membrane. Three sets of rings are seen in this plate along with a parenthesis-shaped ring which is present at a docking site lacking a trichocyst. Pits appear in the rings where the rosettes were removed that remained attached to the E-face of the plasma membrane. TEM taken on 3/6/90 by R. Allen with Zeiss 10A operating at 80kV. Neg. 19,800X. Bar = 0.2µm.
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/j0h99442
title: CIL:36684, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

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; Print from negative scanned for Photoshop.
Data qualification: Processed
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: Following discharge, remnant trichocyst membrane does not appear to directly enter the trans Golgi network for reuse in new trichocyst formation. Rather the HRP will be transferred to lysosomes (not shown) so the membrane presumably becomes part of the lysosomal membrane and eventually part of the phagolysosome digestive vacuole. The HRP content will be subjected to digestion. Exactly what happens to all the excess membrane is unknown although it probably becomes part of the cell‚Äôs overall membrane pool which must be continuously synthesized and replenished as it is halved at each cell division that occurs at 24 hour intervals. TEM taken on 4/12/79 by R. Allen with Hitachi HU11A operating at 75kV. Neg. 14,750X. Bar = 0.25¬µ
DOI: 10.6075/j0rf5t0k
title: CIL:36675, Paramecium multimicronucleatum, cell by organism, eukaryotic cell, Eukaryotic Protist, Ciliated Protist. In Cell Image Library

description: Larger vesicles contain paracrystalline cores that are associated at one end with the trichocyst membrane. This may mean that there is a site on the membrane that promotes paracrystalline formation or that such an association somehow leads to the asymmetric elongated final shape of the trichocyst. TEM taken on 6/7/88 by C. Schroeder with Zeiss 10A operating at 80kV. Neg. 15,900X. Bar = 0.5µm.
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