cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0k64gp2
title: CIL:28771. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
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 0.30 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: 10.6075/j0hq3xk8
title: CIL:28770. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0qj7g0x
title: CIL:28762. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
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 0.30 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: 10.6075/j0rx99rk
title: CIL:28761. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0ft8k2q
title: CIL:2876, 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 0.2% saponin. The fibers were 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.

Images were recorded on Kodak 4489 film at 100,000x 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:2875.
DOI: 10.6075/j04x56f6
title: CIL:28759. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0f18xdd
title: CIL:28758. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0xp752b
title: CIL:35710, Saccharomyces cerevisiae. In Cell Image Library

description: A time lapse experiment of Saccharomyces cerevisiae expressing GFP-tagged NET1. 
 
 NET1 is a core subunit of the RENT complex that involves in nucleolar silencing and telophase exit; stimulates transcription by RNA polymerase I and regulates nucleolar structure.
 
These phase,gfp images are part of an image group that ranges from CIL:35700-35719. Note that there are additional groups showing time series of other cell cycle regulation proteins by the same authors in the Library.
description: Time-lapse images were collected on a DeltaVision system (Olympus IX71) with 60x/1.42 NA objective at 5 minute intervals. Please see the microscopy section in the referenced manuscript for details for image analysis.
description: Preparation: living tissue
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission; elastic scattering of photons
Source of contrast: distribution of a specific protein; differences in amount of elastic light scattering
Visualization methods: EGFP; visualization of contiguous regions
DOI: 10.6075/j01r6p6k
title: CIL:28767. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j00000r9
title: CIL:28766. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
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 0.30 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: 10.6075/j09885p2
title: CIL:28765. In Cell Image Library

description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
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 0.30 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: 10.6075/j0w9588d
title: CIL:2877, 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 0.2% saponin. The fibers were 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.

Images were 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:2878.
DOI: 10.6075/j03f4n98
title: CIL:28728. In Cell Image Library

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 0.60 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0pr7tmw
title: CIL:28726. In Cell Image Library

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 0.60 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image
DOI: 10.6075/j0s75ggz
title: CIL:43751, Homo sapiens, epithelial cell. In Cell Image Library

description: HeLa cells carrying the appropriate EGFP-labeled transgene were fixed in cold methanol, rehydrated, and treated with mouse antibody to alpha-tubulin and goat antibody to GFP followed by donkey-anti-mouse Alexa 594, donkey-anti-goat Alexa 488 and Hoechst 33342. Preparations were examined using a Zeiss Axioplan 2 widefield microscope with a 63x NA 1.4 objective lens. Images were recorded using a CCD camera (CS472-95, Hamamatsu). 
For further details see: Zaliga M et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nat. Cell Biol. published online Feb 2013;DCI:10.1038/ncb2689.
description: Preparation: methanol fixed tissue
Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: differences in adsorption or binding of stain; distribution of epitope
Visualization methods: Hoechst 33342; EGFP; Alexa Fluor 594
Data qualification: Processed;spatialmeasurements
description: Shown is a fluorescence microscopy image of a HeLa cell at mitotic metaphase. The cell is stained to reveal DNA (blue), microtubules (red), and the C-terminal portion of the KIF2A protein (green) which is largely confined to the compact chromosomes.
 The image is part of a large project to characterize the locations of recombinantly tagged kinesin and myosin genes expressed from human or mouse-derived bacterial artificial chromosomes (BACs) as a resource for cell biology research. 
 See also: Maliga et al. 2013 A genomic toolkit to investigate kinesin and myosin motor funtion in cells. Nature Cell Biol; published online Feb 2013;DCI:10.1038/ncb2689.
DOI: 10.6075/j0736pjc
title: CIL:28756. In Cell Image Library

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 0.30 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)."
description: Preparation: first image computer simulation
Relation to intact cell: dispersed cells in vitro
Item type: portrayed image; computational methods
Imaging mode: fluorescence microscopy
Processing history: second image segmentation of simulated image