cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j07m0715
title: CIL:8260, Rattus, multipolar neuron. 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: 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
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.
DOI: 10.6075/j0s181jj
title: CIL:8259, Rattus, multipolar neuron. 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: 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
description: Development of axon and dendritic arbors in cultured hippocampal neurons after 3 days in vitro. At this timepoint, most, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming well 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.
DOI: 10.6075/j00z72b2
title: CIL:8258, Rattus, multipolar neuron. 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: 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
description: Development of axon and dendritic arbors in cultured hippocampal neurons after 3 days in vitro. At this timepoint, most, but not all cells are polarized, evidenced by the absence of a long, slender axon. MAP2 staining (red) is becoming well 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.
DOI: 10.6075/j0js9phr
title: CIL:8060, Rattus norvegicus, permanent cell line cell. In Cell Image Library

description: Traffic Jam: The Dynamic Behavior of a Golgi Matrix Protein

This video shows an NRK cell stably expressing the Golgi matrix protein GRASP55-GFP. The Golgi apparatus in mammalian cells is made up of stacked cisternae organized in a ribbonlike structure within a ribosome-free Golgi matrix. The matrix is composed of coiled-coil proteins, many of which were first identified as autoantigens and termed Golgins. Golgi matrix proteins were thought to be stably associated with the matrix once synthesized, but increasing evidence suggests they are dynamic. By means of high-speed live-cell imaging the video shows the highly dynamic behavior of GRASP55-GFP-containing tubulo/vesicular structures moving in anterograde and retrograde fashion between ER exit sites and the Golgi apparatus.

NRK cells stably expressing GRASP55-GFP and plated on 35-mm glass-bottom culture dishes (MatTek), were maintained in phenol red-free buffered medium at 37C by using an ASI 400 Air Stream stage Incubator (Nevtek, Burnsville, VA). Time-lapse fluorescence images were acquired with an Ultraview Confocal Scanner (Perkin Elmer-Cetus, Norwalk, CT) in a Nikon Eclipse TE2000-S inverted microscope (Nikon, Melville, NY) equipped with a PlanApo 100x oil immersion objective (NA 1.40; Nikon), and a 12-bit charge-coupled device (CCD) camera, ORCA (Hamamatsu, Bridgewater, NJ). Image capture and data acquisition were performed using Ultraview LCI software (Perkin Elmer-Cetus). Images were acquired in binning 2 x 2 modes at approximately 0.25-s intervals, during approximately 120 s. Sequence images were exported as single TIFF files, and processed with ImageJ 1.36b (Rasband, 1997, 2007; http://rsb.info.nih.gov/ij/).

Marra P et al. The GM130 and GRASP65 Golgi proteins cycle through and define a subdomain of the intermediate compartment. Nat Cell Biol [serial online]. 2001;3:1101-1113. 

Mardones GA, Snyder CM, Howell KE. Cis-Golgi matrix proteins move directly to endoplasmic reticulum exit sites by association with tubules. Mol Biol Cell [serial online]. 2006;17:525-38.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: confocal microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: fluorescent protein tag; Green fluorescent proteins from Aequorea
Processing history: non-linear methods
DOI: 10.6075/j0xs5tfd
title: CIL:8059, Rattus norvegicus, permanent cell line cell. In Cell Image Library

description: Brefeldin A (BFA) is a fungal metabolite that reversibly blocks protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus. This effect is accompanied by a distinctive morphological change, the reversible collapse of the Golgi apparatus. The disassembly of the Golgi apparatus is accompanied by its dramatic tubulation, forming a network extending throughout the cytoplasm. While the content of the Golgi apparatus is redistributed to the ER, the content of the trans-Golgi network (TGN) collapses in the vicinity of the MTOC. 

This video shows the effect of BFA in an NRK cell stably expressing GFP-GMx33a, a protein associated to the TGN. 

NRK cells stably expressing GFP-GMx33a and plated on 35-mm glass-bottom culture dishes (MatTek), were treated with 5 microgram/ml BFA and maintained in phenol red-free buffered medium at 37C by using an ASI 400 Air Stream stage Incubator (Nevtek, Burnsville, VA). After 10 minutes in the presence of BFA time-lapse fluorescence images were acquired with an Ultraview Confocal Scanner (Perkin Elmer-Cetus, Norwalk, CT) in a Nikon Eclipse TE2000-S inverted microscope (Nikon, Melville, NY) equipped with a PlanApo 100x oil immersion objective (NA 1.40; Nikon), and a 12-bit charge-coupled device (CCD) camera, ORCA (Hamamatsu, Bridgewater, NJ). Image capture and data acquisition were performed using Ultraview LCI software (Perkin Elmer-Cetus). Images were acquired in binning 2 x 2 modes at approximately 0.25-s intervals, during approximately 175 s. Sequence images were exported as single TIFF files, and processed with ImageJ 1.36b (Rasband, 1997, 2007; http://rsb.info.nih.gov/ij/).

Lippincott-Schwartz J, Donaldson JG, Schweizer A, Berger EG, Hauri HP, Yuan LC, Klausner RD. Microtubule-dependent retrograde transport of proteins into the ER in the presence of brefeldin A suggests an ER recycling pathway. Cell [serial online]. 1990;60:821-36. 

Lippincott-Schwartz J, Yuan L, Tipper C, Amherdt M, Orci L, Klausner RD. Brefeldin A's effects on endosomes, lysosomes, and the TGN suggest a general mechanism for regulating organelle structure and membrane traffic. Cell [serial online]. 1991;67:601-16. 

Snyder CM, Mardones GA, Ladinsky MS, Howell KE. GMx33 associates with the trans-Golgi matrix in a dynamic manner and sorts within tubules exiting the Golgi. Mol Biol Cell [serial online]. 2006;17:511-24.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: confocal microscopy
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of a specific protein
Visualization methods: fluorescent protein tag; Green fluorescent proteins from Aequorea
Processing history: non-linear methods
DOI: 10.6075/j0xw4ht8
title: CIL:8049, Mus musculus. In Cell Image Library

description: Fluorescence recovery after photobleaching (FRAP)kinetics of MeCP2 were recorded using a mouse fibroblast cell line stably expressing MeCP2-GFP. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching two 1 micrometer diameter circles of pericentromeric heterochromatin, followed by 108 images at 2 sec intervals.
description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
DOI: 10.6075/j06972nd
title: CIL:8048, Mus musculus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
description: Fluorescence recovery after photobleaching (FRAP)kinetics of MeCP2 were recorded using a mouse fibroblast cell line stably expressing MeCP2-GFP. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching a 1 micrometer diameter circle of pericentromeric heterochromatin, followed by 102 images at 2 sec intervals.
DOI: 10.15468/dl.4azkyw
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Nepal",
 "OccurrenceStatus is Present",
 "TaxonKey is Rousettus leschenaultii"
 ]
}

 The dataset includes 54 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009683-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0kp81fw
title: CIL:812, Dictyostelium discoideum, cell by organism, eukaryotic cell, amoeboid cell, Eukaryotic Protist. In Cell Image Library

description: This time series stack shows an amoeba (Dictyostelium discoideum) trying very hard to ingest a yeast cell (Saccharomyces cerevisiae) that is slightly too large. (The yeast cell is a mutant with an elongated bud. See note 1.) The amoeba is expressing two fluorescent fusion proteins: GFP-PLCdelta2 (note 2), which binds to phosphatidylinositol 4,5-bisphophate and labels the plasma membrane, and mRFP-LimEdelta (note 3), which labels actin filaments. Actin filaments shape the phagocytic cup at its leading edge and ring it in dynamic bands as it extends deep in the cell. The yeast is too long, and eventually the amoeba gives up, as indicated by the disappearance of the actin filaments. The yeast is promptly expelled with remarkable speed and force, and the excess membrane is converted into ruffles. The motile amoeba contacts the yeast anew, spreads along its length until reaching the end, then tries again to engulf it, but with no better luck. The similarities between a cell spreading on a substratum and forming a phagocytic cup are evident. Methods: Living cells were imaged using a Zeiss LSM 510 laser scanning confocal microscope with standard components and a Zeiss Plan-Apochromat 63x 1.4 N.A. DIC objective. Simultaneous fluorescence images (confocal) and DIC images were recorded from a single focal plane. Scans were performed every 3.89 seconds using a scan zoom of 3.5. References to reagents: 1: S. cerevisiae DDY-1306 (Kozminski, K.G., Chen, A.J., Rodal, A.A., Drubin, D.G. Mol. Biol. Cell 11:339-54, 2000). 2: Green Fluorescent Protein fused to the pleckstrin homology domain of phospholipase C delta-1 (Sauffer, T.P., Ahn, S., and Meyer, T., Curr. Biol. 8:343-346, 1998). 3: Monomeric Red Fluorescent Protein fused to a fragment of Dictyostelium LimE (Fischer, M., Haase, I., Simmeth, E., Gerisch, G., and Muller-Taubenberger, A., FEBS Lett. 577:227-232, 2004). The video received an Honorable Mention in the 2009 Olympus Bioscapes International Digital Imaging Competition and also may be viewed here: http://www.olympusbioscapes.com/gallery/2009/. A movie version of this stack is available in this library at CIL:12654.
description: Preparation: living tissue
Relation to intact cell: living tissue
Item type: fluorescence microscopy; differential interference contrast microscopy
Imaging mode: recorded image; single-spot confocal microscopy; differential interference contrast microscopy
Parameter imaged: single-spot confocal microscopy; differential interference contrast microscopy
Source of contrast: fluorescence microscopy; distribution of a specific protein; boundaries between regions with different refractive index
Visualization methods: fluorescent protein tag; mRFP-LimEΔ - probe for actin filaments; EGFP-PH-PLC-δ1 - binds (4,5)bisphosphate
Processing history: recorded image; NIH Image J
Data qualification: Processed
DOI: 10.6075/j0c828jv
title: CIL:809, Rattus, multipolar neuron. 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: 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
description: During hippocampal neuron development in vitro, N-cadherin becomes selectively localized to excitatory synapses. This image shows synapses that are also immunopositive for the presynaptic glutamate transporters V-glut 1 and 2. Corresponding images in this image group show immunolocalization of N-cadherin, and the postsynaptic NMDA receptor. 
 
Individual fluorescent images were acquired using a Nikon Diaphot 300 with a 60X objective. Preparation was fixed in 4% paraformaldehyde and permeabilized with .01% TritonX-100.
DOI: 10.6075/j0vm4bgb
title: CIL:825, Notophthalmus viridescens, oocyte. In Cell Image Library

description: Amphibian oocytes have many copies of rRNA genes that are actively transcribed. Newt oocyte nuclei were dissected, allowed to swell in a low ionic strength high pH buffer, centrifuged through a sucrose-formaldehyde cushion onto EM grids coated with carbon films, and, in this iamge, stained with aqueous uranly acetate. The strand stretching from top left to bottom right contains two tree-like transcribed genes showing the closely packed RNA polymerases with inceasingly large nascent rRNA transcripts as they approach the termination point. Nascent transcripts are more compact with negative than positive staining. Nucleosomes are visible in the spacer region between transcripts.
description: Preparation: formaldehyde fixed tissue
Relation to intact cell: isolated subcellular component
Item type: microscopy
Imaging mode: transmission electron microscopy (TEM); detection of electrons; film
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: electron-dense stain; visualization of contiguous regions; negative staining; uranyl salt
Processing history: unprocessed raw data
DOI: 10.6075/j07h1hw1
title: CIL:807, Rattus, multipolar neuron. 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: 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
description: During hippocampal neuron development in vitro, N-cadherin becomes selectively localized to excitatory synapses. This image shows immunolocalization of N-cadherin. Other images in this image group show this staining is colocalized at synapses that are also immunopositive for the presynaptic glutamate transporters V-glut 1 and 2 and for the postsynaptic NMDA receptor. 
 
Individual fluorescent images were acquired using a Nikon Diaphot 300 with a 60X objective. Preparation was fixed in 4% paraformaldehyde and permeabilized with .01% TritonX-100.
DOI: 10.6075/j0dj5drd
title: CIL:7914, Mus musculus. In Cell Image Library

description: Preparation: living tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: confocal microscopy
Parameter imaged: fluorescence emission
Source of contrast: quantity of GFP-protein
Visualization methods: Green fluorescent proteins from Anthozoa
Processing history: unprocessed raw data
description: Fluorescence recovery after photobleaching (FRAP)kinetics of histone H1-zero were recorded using mouse fibroblast cell line stably expressing GFP-H10. Live cells were imaged using a Zeiss LSM 510 meta confocal microscope with fluorescence excitation at 488 nm and a 63x plan-apo oil lens. The image series has 2 pre-bleach shots, one immediately after bleaching a 1 micrometer diameter circle of euchromatin, and 47 images at 5 sec intervals.
DOI: 10.6075/j03b5z60
title: CIL:6262, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), 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 11 degrees and visualized in a JEOL 100CX2 transmission electron microscope operated at 100 kev.

The 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:6161.
description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
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
DOI: 10.6075/j0rb74nj
title: CIL:6219, Rattus, multipolar neuron. 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: 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
description: 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 MAP2 (HM2, from Sigma with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch). Images were acquired with a Leica DMRA microscope with a 40X HCX PL APO (1.25 NA) lens, Photometrics CoolSnap ES CCD camera and MetaMorph software. This merged image was generated using the color combine function in Metamorph.
description: Synapse formation in cultured hippocampal neurons after 7 days in vitro. Cells were immunostained for MAP2, a microtubule associated protein localized to dendrites but not axons (green), and synapsin I, a presynaptic vesicle protein (red)to reveal the development of presynaptic contacts along the dendritic arbor.