OpenCCDB version 1.0.0 release notes (6/30/2010)

What’s New in OpenCCDB  1.0

  • Migrated from Oracle DBMS to PostgreSQL DBMS

  • Major redesign of the database schema

    • Integrated with the NIF ontology markup
    • Supports more flexible experimental designs
    • Better support of correlated microscopies
    • Support of "super reconstructions", i.e. a reconstruction of reconstructions
    • Better tracking of subjects across different projects.
    • Better tracking of data set transformations and provenance
    • Better support for automated uploads of image data sets
  • Migrated the collections management system from SRB to IRODS

  • Released high resolution image visualization and annotation tool (Web Image Browser - WIB)

  • Migrated input forms from Gridsphere to Liferay portal

  • Released beta auto-segmentation tool for extracting cellular components from electron micrographs (Cytoseg)

 

Detailed component list

  • New CCDB database schema version 2.2

  • Liferay portal          

    • Imaging product registration v 1.0.4
      •   Browse, create & edit the projects, experiments, microscopy products and subjects
      •   Assign data permissions
      •   View the WIB images upon upload
      •   Launch the upload tool
      •   Launch the data management tool.
    • Project search v 1.0.0
      • Keyword search for the project information
    • Upload tool 1.0.0
      • Upload data to IRODS
      • Report information about the new data
      • Automated conversion to WIB images
    • Data management tool 1.0.0
      • Browse data by CCDB ID
      • Assign the data purpose ID (data role) to the data
      • Tag the data with the keywords and ontology terms
      • Cut and paste data files
      • Launch Cytoseg routines
      • Launch the WIB viewer
    • Detailed data registration
      • Create & edit the detailed microscopy product information including the anatomical description, imaging parameters, image 2D, reconstructions and segmentations.
      • Launch the upload tool
      • Launch the data management tool.
    • Image utilities
      • Downsampler – Efficiently convert and downsample the high resolution images
      • WIB creator -  Create the WIB tiled images
      • Vcutter – Crop and downsample the IMOD volume data
      • Cutter – Slice the volume data as a 2D image
  • WIB 2.0

    • Supported formats
      • The tiled jpeg images (HTTP)
      • PPM (SRB or IRODS)
      • TIFF (SRB or IRODS)
      • PNZ (HTTP)
      • IMOD - .st, .rec, .mrc (SRB or IRODS)
    • Zoom or pan high resolution images
    • Enable or disable color channels
    • Adjust the brightness
    • Adjust the contrast
    • Ontology annotation on the image
    • Sharing the WIB view with the collaborators

 

  • Cytoset beta 1.0.0

    • Support format(s)
      • TIFF images 
    • Generate the automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy

 

Known bugs

 

 

Terms and Conditions:

BSD license

Copyright (c) 2010, CCDB
All rights reserved.

Redistribution and use in source and binary forms are permitted
provided that the above copyright notice and this paragraph are
duplicated in all such forms and that any documentation,
advertising materials, and other materials related to such
distribution and use acknowledge that the software was developed
by the CCDB.  The name of the
University may not be used to endorse or promote products derived
from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

 

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