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Protein Subcellular Location Image Database

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.

URL: http://pslid.org/

Resource ID: nif-0000-33313     Resource Type: Resource     Version: Latest Version

Keywords

protein, structure, subcellular, organelle, image, fluorescence microscope, annotation, classify, rank, cluster, subcellular localization, 3d spatial image, 2d spatial image, micrograph, content-based retrieval, green fluorescent protein

Additional Resource Types

Database, Data Set, Data Repository, Image Analysis Service

Availability

Open access

Publication Link

http://murphylab.web.cmu.edu/publications/85-huang2002.pdf

Abbreviation

PSLID

Synonyms

PSLID - Protein Subcellular Location Image Database, Protein Subcellular Location Image Database

Parent Organization

Funding Information

NIH, NSF, Merck Company Foundation, NIGMS, GM075205, R33 CA83219, MCB-8920118

Listed By

3DVC, Biositemaps

Supercategory

Resource

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

  • Description was changed
  • Additional Resource Types was changed

Version 2

Created 3 weeks ago by Christie Wang

Version 1

Created 5 years ago by Anonymous