cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.647593.v1
title: CIL:27834

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.0 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. Recommended citation We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc).
DOI: 10.6084/m9.figshare.647590
title: CIL:11960

description: This is one of 4 grouped time lapse movies (CIL 11958-11962) revealing the responses of a meiotic oocyte spindle to various forms of micromanipulation by a glass microneedle. The needle is inserted, from below, through the egg cortex to the inner pole of the metaphase spindle. This movie, speeded up about 10-fold, illustrates the ability of the spindle to return to its attachment site at the cell cortex after being moved. The spindle is made visible by the use of polarizing optics.
DOI: 10.6084/m9.figshare.647591.v1
title: CIL:11961

description: This is one of 4 grouped time lapse movies (CIL 11958-11962) revealing the responses of a meiotic oocyte spindle to various forms of micromanipulation by a glass microneedle. The needle is inserted, from below, through the egg cortex to the inner pole of the metaphase spindle. This movie, speeded up about 10-fold, illustrates the positional 'memory' of the system. After the spindle has been moved to the center of the cell, it returns to its original position and orientation. The spindle and its orientation are made visible by the use of polarizing optics.
DOI: 10.6084/m9.figshare.647592.v1
title: CIL:27833

description: One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of five subsets with increasing degree of clustering. Five subsets of 20 images each are provided. Each image contains 300 objects, but the objects overlap and cluster with overlap probability ranging from 0.0 to 0.6, and can be found with CIL 27833, 27853, 28754, 28734, and 28714, respectively. This image set has 0.0 probability overlap. The images were generated with the SIMCEP (http://www.cs.tut.fi/sgn/csb/simcep/tool.html) simulating platform for fluorescent cell population images (Lehmussola et al., IEEE T. Med. Imaging, 2007 and Lehmussola et al., P. IEEE, 2008). Ground truth for foreground/background segmentation are available as binary images as the second image in the tiff image stack. Recommended citation We used the Synthetic 1 image set (Ruusuvuori et al., in Proc. of the 16th European Signal Processing Conference (EUSIPCO-2008), 2008), available from the Broad Bioimage Benchmark Collection (www.broad.mit.edu/bbbc).
DOI: 10.6084/m9.figshare.647587
title: CIL:39753

description: Astrocyte cell from live slices taken from the cortex layer 2/3 of an 8 month old GFAP mouse. In this mouse the enhanced green fluorescent protein (EGFP) under the control of the human glial fibrillary acidic protein (GFAP) promoter (line TgN(GFAP-EGFP)GFEC-FKi). In the image, you can clearly see cell the body, astrocyte cloud and astrocyte projection on vascular tube crossing astrocyte cloud (left and up from cell body). This image an individual z slice. Another z slice is available as CIL 39752, and the projection of 30 slices is available as CIL 30751.
DOI: 10.6084/m9.figshare.647588
title: CIL:42157

description: Time lapse movie of P-cadherin +/- epithelium (mammary organoid) branching normally in 3D collagen I matrix. The movie shows minimal cell dissemination and retention of complete myoepithelial coverage. The cells are expressing td tomato as a membrane marker and eEGFP-actin using a keratin-14 promoter. Images were collected every 20 minutes. Image size is 350 x 350 microns. A movie of a normal mouse mammary organoid in collagen I can be found at CIL 42155. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6084/m9.figshare.647587.v1
title: CIL:39753

description: Astrocyte cell from live slices taken from the cortex layer 2/3 of an 8 month old GFAP mouse. In this mouse the enhanced green fluorescent protein (EGFP) under the control of the human glial fibrillary acidic protein (GFAP) promoter (line TgN(GFAP-EGFP)GFEC-FKi). In the image, you can clearly see cell the body, astrocyte cloud and astrocyte projection on vascular tube crossing astrocyte cloud (left and up from cell body). This image an individual z slice. Another z slice is available as CIL 39752, and the projection of 30 slices is available as CIL 30751.
DOI: 10.6084/m9.figshare.647588.v1
title: CIL:42157

description: Time lapse movie of P-cadherin +/- epithelium (mammary organoid) branching normally in 3D collagen I matrix. The movie shows minimal cell dissemination and retention of complete myoepithelial coverage. The cells are expressing td tomato as a membrane marker and eEGFP-actin using a keratin-14 promoter. Images were collected every 20 minutes. Image size is 350 x 350 microns. A movie of a normal mouse mammary organoid in collagen I can be found at CIL 42155. This movie is part of a group of movies that include CIL 42151-42168.
DOI: 10.6084/m9.figshare.647589
title: CIL:11958

description: This is one of 4 grouped time lapse movies (CIL 11958-11962) revealing the responses of a meiotic oocyte spindle to various forms of micromanipulation by a glass microneedle. The needle is inserted, from below, through the egg cortex to the inner pole of the metaphase spindle. This movie, speeded up about 10-fold, shows the transient puckering in the cell membrane showing that the spindle pole is attached to the cortex. After the attachment has been broken, the cell surface rounds back up. The spindle is made visible by the use of polarizing optics.
DOI: 10.6084/m9.figshare.647590.v1
title: CIL:11960

description: This is one of 4 grouped time lapse movies (CIL 11958-11962) revealing the responses of a meiotic oocyte spindle to various forms of micromanipulation by a glass microneedle. The needle is inserted, from below, through the egg cortex to the inner pole of the metaphase spindle. This movie, speeded up about 10-fold, illustrates the ability of the spindle to return to its attachment site at the cell cortex after being moved. The spindle is made visible by the use of polarizing optics.
DOI: 10.6084/m9.figshare.647584
title: CIL:40422

description: Transmission electron micrograph of a crenated organelle from an untreated sac1∆ mutant cell. This image is a high-magnification zoom of the cell in CIL 40434 (40,000X). This image is part of an image group of cisternae images, CIL: 40417-40423. The contributor asks Library users to post comments regarding whether this structure is part of the Golgi Apparatus or is an immature/abnormal autophagosome.
DOI: 10.6084/m9.figshare.647585
title: CIL:40423

description: Abnormal organelles from a sac1∆ mutant treated with 60µM sertraline. This image is a high-magnification zoom of the cell in CIL 40433. This image is part of an image group of cisternae images, CIL: 40417-40423.
DOI: 10.6084/m9.figshare.647585.v1
title: CIL:40423

description: Abnormal organelles from a sac1∆ mutant treated with 60µM sertraline. This image is a high-magnification zoom of the cell in CIL 40433. This image is part of an image group of cisternae images, CIL: 40417-40423.
DOI: 10.6084/m9.figshare.647586
title: CIL:40440

description: Transmission electron micrograph of a vacuole from a sertraline-treated chc1 mutant cell. This vacuole shows evidence of active autophagy. This image is a high-magnification zoom of the cell in CIL 40415 (16,000X). This image is part of a group of yeast vacuole images (CIL:40437-40448). The image contributor encourages Library users to add comments regarding possible causes the separation between the homogenous electron-opaque contents and the mixed opacity contents.
DOI: 10.6084/m9.figshare.647589.v1
title: CIL:11958

description: This is one of 4 grouped time lapse movies (CIL 11958-11962) revealing the responses of a meiotic oocyte spindle to various forms of micromanipulation by a glass microneedle. The needle is inserted, from below, through the egg cortex to the inner pole of the metaphase spindle. This movie, speeded up about 10-fold, shows the transient puckering in the cell membrane showing that the spindle pole is attached to the cortex. After the attachment has been broken, the cell surface rounds back up. The spindle is made visible by the use of polarizing optics.
DOI: 10.6084/m9.figshare.647583
title: CIL:40419

description: Transmission electron micrograph of crescent-shaped organelles from an arf1∆ mutant cell treated with 60µM sertraline. This image is a high-magnification zoom of the cell in CIL 40411 (25,000X). This image is part of an image group of cisternae images, CIL: 40417-40423. The contributor invites Library users to comment on whether these organelles are related to the endoplasmic reticulum.
DOI: 10.6084/m9.figshare.647586.v1
title: CIL:40440

description: Transmission electron micrograph of a vacuole from a sertraline-treated chc1 mutant cell. This vacuole shows evidence of active autophagy. This image is a high-magnification zoom of the cell in CIL 40415 (16,000X). This image is part of a group of yeast vacuole images (CIL:40437-40448). The image contributor encourages Library users to add comments regarding possible causes the separation between the homogenous electron-opaque contents and the mixed opacity contents.
DOI: 10.6084/m9.figshare.647582
title: CIL:40374

description: This is a higher magnification image of CIL 40371. This is a higher magnification image of CIL 40371.
DOI: 10.6084/m9.figshare.647583.v1
title: CIL:40419

description: Transmission electron micrograph of crescent-shaped organelles from an arf1∆ mutant cell treated with 60µM sertraline. This image is a high-magnification zoom of the cell in CIL 40411 (25,000X). This image is part of an image group of cisternae images, CIL: 40417-40423. The contributor invites Library users to comment on whether these organelles are related to the endoplasmic reticulum.
DOI: 10.6084/m9.figshare.647584.v1
title: CIL:40422

description: Transmission electron micrograph of a crenated organelle from an untreated sac1∆ mutant cell. This image is a high-magnification zoom of the cell in CIL 40434 (40,000X). This image is part of an image group of cisternae images, CIL: 40417-40423. The contributor asks Library users to post comments regarding whether this structure is part of the Golgi Apparatus or is an immature/abnormal autophagosome.
DOI: 10.6084/m9.figshare.647581
title: CIL:39789

description: Scanning electron microscope image of Strongylocentrotus drobachiensus [sea urchin] embryo at the late gastrula stage. This is a high magnification image of CIL 39785. Embryo was cut to reveal blastocoel cavity. The primary mesenchyme cells have formed a syncytial ring, which is the precursor to spicule formation (developing calcareous larval skeleton). This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
DOI: 10.6084/m9.figshare.647579
title: CIL:38604

description: This total internal reflection (TIRF) image of unconverted tdEos-paxillin (green) and PsCFP20-zyxin (red) demonstrates that these two proteins are almost completely colocalized when observed with diffraction limited optics. The true localization pattern is shown in the corresponding photoactivation localization microscopy (PALM) image, CIL 38602. Note the differential interference contrast (DIC) image corresponding to the same image field is also available as CIL 38603. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647580
title: CIL:39785

description: Scanning electron microscope image of Strongylocentrotus drobachiensus [sea urchin] embryo at the late gastrula stage. Embryo was cut to reveal blastocoel cavity. The fertilization envelope dissolves during swimming blastula stage; therefore, the cilia and microvilli can be seen on the outer epithelial layer. The primary mesenchyme cells have formed a syncytial ring, which is the precursor to spicule formation(developing calcareous larval skeleton). A portion of the archenteron can also be seen. A high magnification view of a region of this image is available as CIL:39789. This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
DOI: 10.6084/m9.figshare.647581.v1
title: CIL:39789

description: Scanning electron microscope image of Strongylocentrotus drobachiensus [sea urchin] embryo at the late gastrula stage. This is a high magnification image of CIL 39785. Embryo was cut to reveal blastocoel cavity. The primary mesenchyme cells have formed a syncytial ring, which is the precursor to spicule formation (developing calcareous larval skeleton). This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
DOI: 10.6084/m9.figshare.647582.v1
title: CIL:40374

description: This is a higher magnification image of CIL 40371. This is a higher magnification image of CIL 40371.
DOI: 10.6084/m9.figshare.647578
title: CIL:38603

description: This differential interference contrast image (DIC) corresponds to the same image field as the total internal reflection (TIRF) image CIL 38604 and the 2-color photoactivation localization microscopy (PALM) image CIL 38602. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647577
title: CIL:38602

description: This photoactivation localization microscopy (PALM) image of tdEos-paxillin (green) and PsCFP20-zyxin (red) demonstrates that these two focal adhesion proteins are have very little over-lap when visualized with super-resolution. In contrast, when the same field is visualized with total internal reflection (TIRF) microscopy, the two proteins appear almost completely colocalized CIL 38604. Note the differential interference contrast (DIC) image corresponding to the same image field is also available as CIL 38603. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647579.v1
title: CIL:38604

description: This total internal reflection (TIRF) image of unconverted tdEos-paxillin (green) and PsCFP20-zyxin (red) demonstrates that these two proteins are almost completely colocalized when observed with diffraction limited optics. The true localization pattern is shown in the corresponding photoactivation localization microscopy (PALM) image, CIL 38602. Note the differential interference contrast (DIC) image corresponding to the same image field is also available as CIL 38603. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647580.v1
title: CIL:39785

description: Scanning electron microscope image of Strongylocentrotus drobachiensus [sea urchin] embryo at the late gastrula stage. Embryo was cut to reveal blastocoel cavity. The fertilization envelope dissolves during swimming blastula stage; therefore, the cilia and microvilli can be seen on the outer epithelial layer. The primary mesenchyme cells have formed a syncytial ring, which is the precursor to spicule formation(developing calcareous larval skeleton). A portion of the archenteron can also be seen. A high magnification view of a region of this image is available as CIL:39789. This image is part of a group of SEM images of sea urchin embryos at various stages of development. The group is available as CIL:39782-39791.
DOI: 10.6084/m9.figshare.647576
title: CIL:38598

description: Photoactivation localization microscopy image (PALM) of a human foreskin fibroblast expressing Dronpa-alpha-actinin (red) and tdEos-vinculin (green). This image reveals that although conventional diffraction limited microscopy indicates alpha-actinin and vinculin colocalize in focal adhesions, PALM clearly shows that they these molecules are spatially segregated. The DIC corresponds to the same image field is CIL 38597 and the diffraction limited TIRF image is CIL 38599. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 2 in PNASi U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647578.v1
title: CIL:38603

description: This differential interference contrast image (DIC) corresponds to the same image field as the total internal reflection (TIRF) image CIL 38604 and the 2-color photoactivation localization microscopy (PALM) image CIL 38602. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 4 in PNAS U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647573
title: CIL:34928

description: Localization of cross-linking proteins in fibroblast cytoskeleton. mmuno-EM of the cell interior or cell edge (CIL 34925) of cytochalasin D-treated Xenopus fibroblasts stained with p21 (Arp2/3) primary antibody and 10-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal Arp2/3 complex at Y-junctions at cell edge. Fluorescence microscopy and corresponding intensity profiles double stained with TRITC-phalloidin (red) and p21 antibodies (green) is available at CIL 34922. Image corresponds to Figure 5g from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647574
title: CIL:34929

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell interior at cell edge (CIL 34926) of cytochalasin D-treated human 356 fibroblasts stained with ABP-280 primary antibody and 10-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal ABP-280 at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and ABP-280 (green) can be found at (CIL 34923). Image corresponds to Figure 5h from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647575
title: CIL:34930

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell interior at cell edge (CIL 34926) of cytochalasin D-treated Xenopus fibroblasts stained with α-actinin primary antibody and 18-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal α-actinin at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and either α-actinin (green) is available at CIL 34924. The image corresponds to Figure 5f from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647573.v1
title: CIL:34928

description: Localization of cross-linking proteins in fibroblast cytoskeleton. mmuno-EM of the cell interior or cell edge (CIL 34925) of cytochalasin D-treated Xenopus fibroblasts stained with p21 (Arp2/3) primary antibody and 10-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal Arp2/3 complex at Y-junctions at cell edge. Fluorescence microscopy and corresponding intensity profiles double stained with TRITC-phalloidin (red) and p21 antibodies (green) is available at CIL 34922. Image corresponds to Figure 5g from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647576.v1
title: CIL:38598

description: Photoactivation localization microscopy image (PALM) of a human foreskin fibroblast expressing Dronpa-alpha-actinin (red) and tdEos-vinculin (green). This image reveals that although conventional diffraction limited microscopy indicates alpha-actinin and vinculin colocalize in focal adhesions, PALM clearly shows that they these molecules are spatially segregated. The DIC corresponds to the same image field is CIL 38597 and the diffraction limited TIRF image is CIL 38599. Bar is 2 microns. Image made available by Catherine and James Galbraith and corresponds to Figure 2 in PNASi U S A. 2007 Dec 18;104(51):20308-13.
DOI: 10.6084/m9.figshare.647572
title: CIL:34927

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell edge or interior (CIL 34929) of cytochalasin D-treated Xenopus fibroblasts stained with α-actinin primary antibody and 18-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal α-actinin at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and either α-actinin (green) is available at CIL 34924. The image corresponds to Figure 5f from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647575.v1
title: CIL:34930

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell interior at cell edge (CIL 34926) of cytochalasin D-treated Xenopus fibroblasts stained with α-actinin primary antibody and 18-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal α-actinin at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and either α-actinin (green) is available at CIL 34924. The image corresponds to Figure 5f from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647570
title: CIL:34925

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell edge or interior (CIL 34928) of cytochalasin D-treated Xenopus fibroblasts stained with p21 (Arp2/3) primary antibody and 10-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal Arp2/3 complex at Y-junctions at cell edge. Fluorescence microscopy and corresponding intensity profiles double stained with TRITC-phalloidin (red) and p21 antibodies (green) is available at CIL 34922. Image corresponds to Figure 5d from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647571
title: CIL:34926

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell edge or interior (CIL 34929) of cytochalasin D-treated human 356 fibroblasts stained with ABP-280 primary antibody and 10-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal ABP-280 at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and ABP-280 (green) can be found at (CIL 34923). Image corresponds to Figure 5e from J Cell Biol. 1999 May 31;145(5):1009-26.
DOI: 10.6084/m9.figshare.647572.v1
title: CIL:34927

description: Localization of cross-linking proteins in fibroblast cytoskeleton. Immuno-EM of the cell edge or interior (CIL 34929) of cytochalasin D-treated Xenopus fibroblasts stained with α-actinin primary antibody and 18-nm gold-conjugated secondary antibody. Gold particles (yellow) reveal α-actinin at filament crossovers in the cell interior. A fluorescence image of fibroblast lamellipodia double stained with TRITC-phalloidin (red) and either α-actinin (green) is available at CIL 34924. The image corresponds to Figure 5f from J Cell Biol. 1999 May 31;145(5):1009-26.