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Resource:Protein Subcellular Location Image Database

Name: Resource:Protein Subcellular Location Image Database
Description: Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees for the following data sets:
  • 3D images of 90 clones of randomly CD-tagged 3T3.
  • 2D images of 175 clones of randomly CD-tagged 3T3, for p-value thresholds used to select features of 0, 0.1, and 0.2.
  • 3D images of wildtype and 11 mutants of GFP-tagged UCE in HeLa cells.

PSLID collects and structures 2-D through 5-D fluorescence microscope images, annotations, and derived features in a relational schema. It is designed so that interpretations as well as annotations can be queried. The annotations in PSLID, composed of 44 linked tables with publicly available descriptions, provide a thorough description of sample preparation and fluorescence microscope imaging.

Image interpretation is achieved using Subcellular Location Features that have been shown to be capable of recognizing all major subcellular structures and of resolving patterns that cannot be distinguished by eye.

The fundamental unit of PSLID is an image set, which is simply a logical grouping of images. Image sets can be defined at the time of image loading, or they can be defined by searching for images that meet specified criteria (e.g., all images of "actin" or all images that are similar to a query image). They can also be created by analysis functions such as cluster analysis (e.g., the images in each cluster found by cluster analysis can be put into distinct sets).

Analysis capabilities that are incorporated in PSLID include:

  • Searching for images by context (annotations) or content
  • Ranking images by typicality within a set: e.g., to choose an image for presentation or publication
  • Ranking images by similarity to one or more query images: "searching by image content" or "relevance feedback"
  • Comparing two sets of images (hypothesis testing): e.g., to determine whether a drug alters the distribution of a tagged protein
  • Training a classifier to recognize subcellular patterns
  • Using a trained classifier to assign images to pattern classes: e.g., assigning images to "positive" or "negative"
  • Clustering images by their subcellular patterns: e.g., finding "subcellular location families" within a large set of images
Submission to PSLID of other image collections documenting the subcellular location of proteins to facilitate "one-stop" searching for information on subcellular patterns is encouraged.
Other Name(s): PSLID - Protein Subcellular Location Image Database, Protein Subcellular Location Image Database
Abbreviation: PSLID
Parent Organization: Carnegie Mellon University; Pennsylvania; USA
Supporting Agency: National Institute of General Medical Sciences, NIH, NSF, Merck Company Foundation
Grant: GM075205, R33 CA83219, MCB-8920118
Resource Type(s): Database, Data set, Data repository, Image analysis service
Resource: Resource
URL: http://pslid.org/
Id: nif-0000-33313
Publication link: http://murphylab.web.cmu.edu/publications/85-huang2002.pdf
Related to: Resource:Biositemaps, Resource:3DVC
Availability: Open access
Address: Department of Biological Sciences and Center for Automated Learning and Discovery, CarnegieMellon University, 4400 Fifth Avenue, Pittsburgh PA 15213, USA
Keywords: mutant, protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, fluorescence microscope, subcellular location protein, 3D spatial image, 2D spatial image, micrograph
Link to OWL / RDF: Download this content as OWL/RDF

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Facts about Resource:Protein Subcellular Location Image DatabaseRDF feed
AbbrevPSLID  +
AddressDepartment of Biological Sciences and Center for Automated Learning and Discovery  +, CarnegieMellon University  +, 4400 Fifth Avenue  +, Pittsburgh PA 15213  +, and USA  +
AvailabilityOpen access  +
CurationStatusuncurated  +
DefiningCitationhttp://pslid.org/  +
DefinitionAnnotated database of fluorescence microsc Annotated database of fluorescence microscope images depicting subcellular location proteins with two interfaces: a text and image content search interface, and a graphical interface for exploring location patterns grouped into Subcellular Location Trees for the following data sets:
  • 3D images of 90 clones of randomly CD-tagged 3T3.
  • 2D images of 175 clones of randomly CD-tagged 3T3, for p-value thresholds used to select features of 0, 0.1, and 0.2.
  • 3D images of wildtype and 11 mutants of GFP-tagged UCE in HeLa cells.

PSLID collects and structures 2-D through 5-D fluorescence microscope images, annotations, and derived features in a relational schema. It is designed so that interpretations as well as annotations can be queried. The annotations in PSLID, composed of 44 linked tables with publicly available descriptions, provide a thorough description of sample preparation and fluorescence microscope imaging.

Image interpretation is achieved using Subcellular Location Features that have been shown to be capable of recognizing all major subcellular structures and of resolving patterns that cannot be distinguished by eye.

The fundamental unit of PSLID is an image set, which is simply a logical grouping of images. Image sets can be defined at the time of image loading, or they can be defined by searching for images that meet specified criteria (e.g., all images of "actin" or all images that are similar to a query image). They can also be created by analysis functions such as cluster analysis (e.g., the images in each cluster found by cluster analysis can be put into distinct sets).

Analysis capabilities that are incorporated in PSLID include:

  • Searching for images by context (annotations) or content
  • Ranking images by typicality within a set: e.g., to choose an image for presentation or publication
  • Ranking images by similarity to one or more query images: "searching by image content" or "relevance feedback"
  • Comparing two sets of images (hypothesis testing): e.g., to determine whether a drug alters the distribution of a tagged protein
  • Training a classifier to recognize subcellular patterns
  • Using a trained classifier to assign images to pattern classes: e.g., assigning images to "positive" or "negative"
  • Clustering images by their subcellular patterns: e.g., finding "subcellular location families" within a large set of images
Submission to PSLID of other image collections documenting the subcellular location of proteins to facilitate "one-stop" searching for information on subcellular patterns is encouraged.
ion on subcellular patterns is encouraged.
ExampleImagePSLID.PNG  +
GrantCategory:GM075205   +, Category:R33 CA83219   +, and Category:MCB-8920118   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +, Data set  +, Data repository  +, and Image analysis service  +
Idnif-0000-33313  +
Is part ofCarnegie Mellon University; Pennsylvania; USA  +
KeywordsMutant  +, Protein  +, Structure  +, Subcellular  +, Organelle  +, Image  +, Fluorescence microscope  +, Annotation  +, Classify  +, Rank  +, Cluster  +, Subcellular location protein  +, 3D spatial image  +, 2D spatial image  +, and Micrograph  +
LabelResource:Protein Subcellular Location Image Database  +
ModifiedDate17 June 2013  +
Page has default formThis property is a special property in this wiki.Resource  +
PublicationLinkhttp://murphylab.web.cmu.edu/publications/85-huang2002.pdf  +
RelatedToResource:Biositemaps  +, and Resource:3DVC  +
SuperCategoryResource  +
Supporting AgencyNational Institute of General Medical Sciences  +, NIH  +, NSF  +, and Merck Company Foundation  +
SynonymPSLID - Protein Subcellular Location Image Database  +, and Protein Subcellular Location Image Database  +