cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0zp44vd
title: CIL:13724, Homo sapiens, endothelial cell. In Cell Image Library

description: Expression of R98F PINK1-YFP (green) induces mitochondrial translocation of mCherry-Parkin (red) in the presence of the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone), indicating that this PINK1 mutant is functional for inducing Parkin translocation when located on the outer michondrial membrane. The R98F mutation in PINK1-YFP partially inhibits proteolytic cleavage. Transfected HeLa cells were treated with CCCP (10 µM) for 1 hr. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4e, bottom row, with DMSO control in Fig 4e, top row of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
description: Preparation: living 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: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0dv1hk0
title: CIL:13733, Homo sapiens, endothelial cell. In Cell Image Library

description: Mitochondria in HeLa cells are identified by mito-YFP (green). When fixed cells are unpermeabilized (not treated with detergent), antibodies to cyctochrome c (red), a mitochondrial matrix marker, and Tom20 (white), a mitochondrial outer membrane marker, are unable to reach and bind their epitopes. Mito-YFP transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and not permeabilized. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, top row and is a control experiment for a differential permeabilization assay with and without the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone) that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
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: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0183604
title: CIL: 52093, 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/j0445k74
title: CIL:13723, Homo sapiens, endothelial cell. In Cell Image Library

description: Expression of R98F PINK1-YFP (green), consistent with localization within mitochondria, does not induce mitochondrial translocation of mCherry-Parkin (red). The R98F mutation in PINK1-YFP partially inhibits proteolytic cleavage. Transfected HeLa cells were treated with DMSO for 1 hr. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4e, top row, and is a control for Fig 4e, bottom row of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
description: Preparation: living 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: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0p26wvk
title: CIL:13726, Mus musculus, fibroblast. In Cell Image Library

description: Expression of WT PINK1-YFP (green) does not induce mitochondrial translocation of mCherry-Parkin (red) in PINK1 knock-out mouse embryonic fibroblasts (PINK1 KO MEFs). Transfected PINK1 KO MEFs were treated with DMSO for 3 hrs. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Supplemental Figure S1c, top left row of J Cell Biol, 191: 933-942, 2010. Images in Supplemental Figure S1c include CIL#s 13725, 13726, 13727, 13728.
description: Preparation: living 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: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0zs2v6v
title: CIL:10078, Mus musculus, skeletal muscle cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; glutaraldehyde fixed tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: transmission electron microscopy (TEM); electron density
Parameter imaged: electron density
Source of contrast: differences in adsorption or binding of stain
Visualization methods: uranyl salt; lead salt
description: Mouse skeletal muscle. This image depicts a transmission electron micrograph of 1 month old mouse skeletal muscle tissue from the EDL muscle. Note the highly ordered organization of the contractile apparatus. From Gokhin et al JCB 2010, figure 4a.
DOI: 10.6075/j0028q70
title: CIL:13725, Mus musculus, fibroblast. In Cell Image Library

description: Preparation: living 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: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Expression of transmembrane domain deleted-PINK1-YFP (green) is stabilized in the mitochondira, but does not induce mitochondrial translocation of mCherry-Parkin (red) in PINK1 knock-out mouse embryonic fibroblasts (PINK1 KO MEFs). Transfected PINK1 KO MEFs were treated with DMSO for 3 hrs. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Supplemental Figure S1c, top right row of J Cell Biol, 191: 933-942, 2010. Images in Supplemental Figure S1c include CIL#s 13725, 13726, 13727, 13728.
DOI: 10.6075/j00864c2
title: CIL:6555, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: glutaraldehyde fixed tissue; freeze_fracture/freeze_etch
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were held at constant length and rigor induced by immersion in glycerol. The fibers were fixed in buffered glutaraldehyde, treated with tannic acid and quick-frozen by contact with a liquid helium-cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 24 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 75,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6554.
DOI: 10.6075/j0hh6jjb
title: CIL: 51291, 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/j03x85cq
title: CIL:13734, Homo sapiens, endothelial cell. In Cell Image Library

description: Mitochondria in HeLa cells are identified by mito-YFP (green). When fixed cells are permeabilized with 0.25% Triton X-100 (TX-100), both antibodies to cyctochrome c (red), a mitochondrial matrix marker, and the antibody to Tom20 (white), a mitochondrial outer membrane marker, are able to bind their epitopes. Mito-YFP transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.25% Triton X-100/PBS. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, 3rd row from top and is part of a differential permeabilization assay with and without the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone) that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
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 emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j0v69h9x
title: CIL:13729, Homo sapiens, endothelial cell. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: single-spot confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
description: Mitochondria in HeLa cells are identified by mito-YFP (green). When fixed cells are permeabilized with 0.005% digitonin, the antibody to cyctochrome c (red), a mitochondrial matrix marker, is unable to reach and bind cytochrome c, but the antibody to Tom20 (white), a mitochondrial outer membrane marker, is now able to bind Tom20. Mito-YFP transfected HeLa cells were treated with DMSO for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.005% digitonin/PBS. Primary antibodies used were: anti-Cyt c mAb (BD) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4b, 2nd row from top and is part of a differential permeabilization assay with and without the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone) that is further described in Fig 4b of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
DOI: 10.6075/j0gb22tk
title: CIL:13728, Mus musculus, fibroblast. In Cell Image Library

description: Upon mitochondrial uncoupling, transmembrane domain-deleted PINK1-YFP (green) fails to recruit mCherry-Parkin (red) to mitochondria in PINK1 knock-out mouse embryonic fibroblasts (PINK1 KO MEFs). Transfected PINK1 KO MEFs were treated with the mitochondrial depolarizing agent CCCP (carbonyl cyanide-m-chlorophenyl hydrazone) (10µM) for 3 hours. Live cell imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Supplemental Figure S1c, bottom right row of J Cell Biol, 191: 933-942, 2010. Images in Supplemental Figure S1c include CIL#s 13725, 13726, 13727, 13728.
description: Preparation: living 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: EYFP; mCherryFP
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation
DOI: 10.6075/j07p8xhf
title: CIL:9169, Homo sapiens, permanent cell line cell, epithelial cell. In Cell Image Library

description: Preparation: unfixed tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Parameter imaged: fluorescence microscopy
Source of contrast: distribution of a specific protein
Visualization methods: EGFP
Processing history: unprocessed raw data
description: Sialyl Transferase-EGFP transfected HeLa cells demonstrating the redistribution of the Golgi Apparatus to the Endoplasmic Reticulum upon treatment with Brefeldin A (BFA). 
Images were collected as a 4D time series (z-stack over time). z-stacks of 48 individual timepoints are included in this collection of files as well as the movie SiEGFP_BFA.avi, which is the maximum projection of the z-stacks at the individual time points.

BFA was added according to the following protocol:
Timepoint1: Before addition of BFA 0seconds (8 Z-slices at 1 um apart)
Timepoint2: After addition of BFA 130seconds (8 Z-slices at 1 um apart) 
Timepoint3: 238 seconds (11 Z-slices at 1 um apart) 
Timepoint3 thru Timepoint48: Images captured every 5 seconds (11 Z-slices at 1 um apart at each time point) 

Images were collected on a Carl Zeiss spinning disk confocal with a 63X 1.4 NA objective with 250 ms exposures at 5 s intervals.
DOI: 10.6075/j0j965fp
title: CIL:8475, Rattus, multipolar neuron. In Cell Image Library

description: Development of axon and dendritic arbors in cultured hippocampal neurons after 2 days in vitro. At this timepoint, many, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming segregated to the dendrites, while microtubule staining (green) reveals both the axons and dendrites in the field of view. Nonneuronal cells (e.g. glia) are infrequent, but may also be present in this preparation. 

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), permeabilized with 0.25% Triton and immunostained for tubulin (monoclonal DM1A, from Sigma with Alexa 488 conjugated secondary, excitation, 494, emission, 519 [Invitrogen, Molecular Probes]) and MAP2 (polyclonal Ab266, from S. Halpain with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X (HCX PL APO, NA 1.25) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated with the MetaMorph color combine function.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Raw;spatialmeasurements
DOI: 10.6075/j09s1prp
title: CIL:13722, Homo sapiens, endothelial cell. In Cell Image Library

description: YFP-WT PINK1 (green) shows mitochondrial localization in HeLa cells following treatment with the mitochondrial depolarizing agent CCCP (carbonyl cyanide m-chlorophenyl hydrazone). When fixed cells are permeabilized with 0.25% Triton X-100 (TX-100), the antibody to GFP (red) (used to identify YFP-WT PINK1) and the antibody to Tom20 (white), a mitochondrial outer membrane marker, are able to bind their epitopes. This demonstrates that when mitochondrial membrane potential is dissipated, YFP-WT PINK1 accumulates on the outer mitochondrial membrane. YFP-WT PINK1 transfected HeLa cells were treated with CCCP (10µM) for 3 hrs, fixed with 4% paraformaldehyde and permeabilized with 0.25% Triton X-100. Primary antibodies used were: anti-GFP polyclonal Ab (Invitrogen) and anti-Tom20 mAb (BD); secondary antibodies used were: Alexa Fluor 594 and 647. Imaging was performed on an LSM510 Meta (Carl Zeiss, Inc) with a 63x 1.4 NA oil differential interference contrast Plan Apo objective. Image contrast and brightness were adjusted in the LSM image browser (Zeiss). This image corresponds to Fig 4c, 3rd row from top, and is part of a differential permeabilization assay to determine submitochondrial localization of PINK1 and that is further described in Fig 4c of J Cell Biol, 191: 933-942, 2010. Images in Fig 4 include CIL#s 13733, 13734, 13729, 13730, 13731, 13732, 13717, 13718, 13719, 13720, 13721, 13722, 13723, 13724.
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 emission
Source of contrast: distribution of a specific protein
Visualization methods: EYFP; primary antibody plus labeled secondary antibody
Processing history: brightness and contrast adjusted
Data qualification: Raw;spatialmeasurements;intensitiesquantitation