CCDB Search and Display

  Through the Webpage


To search the CCDB, click on the Advanced Search link on the menu bar. No account is required for log in.

The following form will be displayed:

Enter a term in the Keyword field. The CCDB Dictionary contains a listing of current data in the CCDB and may be used as a guide for selecting keywords. To access the Dictionary, click on the Dictionary link on the menu bar.

Users may also browse certain types of files using the Browse menu. Currently, only the All Records link is active. Future versions will allow selection of certain types of data. Clicking on this link will display a summary of all CCDB records.

Search Results Page

The CCDB search returns a set of records that matches the search term. The search summary page presents a subset of the descriptive data and a set of thumbnails for each data set. Users may browse through the results using the scroll bar and the page navigation at the bottom of the search results. The following fields are provided in the search summary page:

1) Selection Box: The new CCDB display pages introduce the concept of MyLabBench which is equivalent to the “Shopping Cart” for on-line purchases. Adding a dataset to MyLabBench will allow users to view a subset of the returned results and identifies data sets for download.

2) ID: The accession number for each dataset. The CCDB assigns a single accession number to all of the data products stored for a single dataset. This ID can be used to identify a data record in the CCDB.

3) Cell Type: The type of cell contained in the image or from which a subcellular structure was obtained, if known

4) Structure: The type of subcellular structure or structures contained in the image

5) MPT: Microscopy Product Type. The MPT refers to the type of data set that was collected for further reconstruction. The CCDB Dictionary contains descriptions of each of the categories.

6) Thumbnails: a representative 2D image supplied by the data provider to describe the contents of the dataset. If no thumbnail is displayed, this type of image data is likely not available for this dataset. Three types of image data are displayed:

a. Raw Image: the set of 2D images that were used to create a 2D, 3D or 4D reconstruction.

b. Reconstruction: a larger 2D, 3D or 4D dataset produced from the raw data.

c. Segmentation: A set of objects or abstractions derived from the reconstruction data for analysis or visualization purposes. Segmented objects may represent surfaces, subvolumes, skeletons or signal distributions.

1) Select a dataset to obtain the full record by clicking on the ID number

2) Identify a set of data for further review and possible download, by selecting the box in the first column

3) Start a new search by clicking on the LiteSearch link in the New Search box in the upper left panel

4) Browse all records by clicking on the All records link in the Browse box in the middle left panel

5) View the contents of MyLabBench by clicking on the link in Current Session box in the lower left panel

6) Go back to the original search results by clicking on the Back to search result link in Current Session box in the lower left panel

Detailed Results Display

Clicking on the ID link will return detailed results for a single dataset.

 

The detailed display page provides a more detailed summary of a datasets and lets the user explore additional descriptive data, view larger versions of the images, view animations and analysis data. The CCDB ID and the image basename are provided in orange next to the header. The image basename is a user supplied identifier for a given dataset that maps to a single CCDB ID. The search terms used to retrieve the data are highlighted in yellow, both on the main page and any additional pages visited for that set. Users may choose to display all details by clicking on the View all details link at the bottom of the main display page, or to navigate through different types of information by using the navigation links in the Data set information box in the upper left panel. CCDB groups information under the following categories:

1) Project info: Information about the project, experiment, subject groups, subjects and specimen.

2) Specimen preparation info: Detailed protocols specifying how the specimen was prepared for imaging. This portion of the CCDB is currently undergoing revision and is not available at this time.

3) Microscopy Product Information: Displays general information on how the images were acquired and larger versions of the thumbnails for the raw data

4) Imaging Product Type: Displays detailed information about the type of image set acquired, e.g., tilt series information, time series information

5) Specimen description: Provides the anatomical details for the image set acquired, e.g., system, organ, cell type, structure

6) Imaging parameters: Provides detailed information on microscope settings during acquisition

7) Reconstruction info: Provides details and images on the reconstruction, including animations and larger versions of the thumbnails

8) Segmentation info: Provides details, analysis results and images for segmented data

From any page, users may return to the original search results by clicking on the Back to search result link in the Session info box on the left lower panel.


Users may click on the thumbnail images provided in the display panel at the top of the page to display higher resolution images and detailed information.

This panel also contains links to additional images that may be useful for interpreting the data, e.g., Map location images locates the target feature within a larger context, e.g., a brain atlas. For some types of data, additional image navigation is provided through the Neuroinformatica software (Microbrightfield, Inc). Neuroinformatica provides easy web-based -navigation across large, high resolution images. Users can pan and zoom light microscopic resolution-limited large brain maps (Price et al., 2006). In a future release, CCDB will integrate the annotation capabilities of Neuroinformatica with the CCDB.

 

 Through the Portal

Data that is entered through the CCDB input forms is assumed to be private data unless specifically released to the public site. To view private data, click on the View data link on the side navigation bar under the Detailed Data Input tab.

Searching for data

CCDB provides two search functions inside the portal: a simple project search and a complete CCDB search. The simple project search is provided in the Register microscopy product form and provides a limited search of the project tables (the first 8 tables) for the purposes of selecting a project during microscopy product registration. The second search function CCDB Complete Search may be accessed from the CCDB Search Engine tab.

This function searches not just the project tables, but all of the image and specimen preparation tables as well. This tool can also be used to set permissions for data sharing, which will be detailed in the next section. Unlike the search result from the website, the portal search tool returns a set of fields from each record that contain the search term so that users can quickly and easily browse through the data and understand the relevance of each search result.


If the appropriate data input and display images have been entered, clicking on the link at the top of the record will open a display page in MyCCDB (see above). The record will indicate whether not enough information has been entered for web display.

Setting Permissions for Viewing and Editing Datasets

For each dataset entered into the CCDB, a user may choose to keep it completely private or may choose to share it with selected colleagues or a group of colleagues. Users may manage the permissions for their data using the CCDB permission tool. To access this tool, users first perform a search through the Complete CCDB Search form, as detailed in the previous section. For each dataset returned, users may change permissions by clicking on the Set Permissions button at the end of each record. The CCDB Data Access Control tool allows the user to assign read, write and edit permission to an individual or a group. Groups may be pre-existing or may be defined by the user. Three levels of authorization may be granted:

•  Read : Permission to view the dataset but not make any changes

•  Write : Permission to add to the dataset but not change existing information

•  Edit : Permission to delete or change existing information and add new information.

The Data Access Control panel displays a list of individuals or groups currently granted access to the selected dataset and their current level of access in the Current Status panel. In the example given above, no other individuals or groups have been given access to this dataset. To assign permissions, users may select from the Available Groups, listed in the top panel, and Available Users listed in the second panel.


Individual access

To change the level of access to a dataset for an individual:

•  Go to the Available users panel

•  Select a user name from the User name pull down menu

•  Click on a level of access ( write or edit )

•  Click on the Add button. The individual or group will now appear in the Current Status pane with a Ö next to active access privileges.

•  Click Remove in the Current Status panel to remove privileges from an individual

Group access

To change the level of access for a group of individuals, perform the above steps using the Group Access panel. Available groups are listed by Group name and by individuals within the group. Users may add or remove members from an existing group or define a new group. Only the person who created the group may add or subtract from an existing group.

To add or remove members from a group:


•  Go to the Organize group members panel and select the group to edit from the Groups pull down menu

•  Remove existing members by selecting the user name from the top pull down menu under Members next to the Remove button

•  Click on Remove

•  Add members by selecting a user name from the bottom pull down menu next to the Add button

•  Click on Add

To create a group:

•  Go to the Create/Delete a group panel

Type in a group name in the box next to the Create button


Go to the Organize group members panel

Select the newly created group from the pull down menu under Groups

Select the members from the pull down menu under Members and click Add


Data Input to the CCDB through the Telescience Portal

The CCDB provides a powerful data management system for reconstruction from light and transmission electron microscopy. Version 1.0 of the CCDB data input forms was released in February 2006. Currently, all data input to the CCDB is performed through the Telescience Portal. The process of data entry into the CCDB consists of the following general steps:

  1. Preparing full resolution image data and analysis files for loading into the CCDB
  2. Preparing lower resolution images and animations for display in the CCDB
  3. Associating these data and image files with the appropriate experimental, imaging and analysis details

The CCDB divides the process of data entry into two steps. The first step assigns a unique accession number to the set of images acquired on the microscope (referred to as the Microscopy Product ) and associates a given data set with the appropriate project and experimental details. This step is referred to as Basic Data Input . The second step adds imaging, detailed specimen preparation, reconstruction and analysis details to the microscopy product. This step is referred to as Detailed Data Input .

Required Data

The following types of data files may be stored in the CCDB:

•  Raw imaging files, e.g., tilt series

•  Reconstructions, e.g., tomograms, mosaics, time series

•  Segmentations, e.g., Surfaces, subvolumes

•  Animations

•  2D representative images

•  Analysis data, e.g., measurements

Descriptive data ("metadata") accompanies each of these data types that provides details on project, experiment, subject, tissue processing, imaging, reconstruction and segmentation. More information on preparing these files for entry can be in the Preparing Data for Input into CCDB section.

Basic Data Input into the CCDB

The CCDB assigns a unique ID to each "microscopy product". The microscopy product is used to describe a set of related images. These images may be related in a systematic way, e.g., tilt series, optical section series, serial section, time series, mosaic, or they may be a set of survey images that were taken of the same specimen at the same time. The microscopy product ID serves as the accession number for a data set. Microscopy product ID's can be obtained before any imaging data is acquired. Because the ID is unique, any data products labeled with this ID, e.g., negatives, can be associated with the appropriate set of details.

Each microscopy product must be registered to a Project , which is the highest level of organization in the CCDB, Experiment, Subject Group, Subject, Specimen . These details are contained in the following tables:

Project:

name, description, leader, funding agency, project starting data, project ending data, collaborators, publications etc.

Experiment:

experiment title, experiment purpose, experiment date, experimenter, etc.

Subject Group :

subject group name, group by and treatment information.

Subject:

species, scientificname, strain, transgenic id

Animal and Cultured Cell:

ageclass, age, sex, weight

Culture type, cell type, plating conditions

Tissue:

anatomic location, tissueprodstorage, microtome, thickness, orientation

Processing:

Protocol and tissue group type

Microscopy Product : basic information about the imaging data

Thus, the first 8 tables create a project hierarchy which provides a summary of a project and assigns each microscopy product to a unique hierarchy. Each level in the hierarchy has a "one to many" relationships, i.e., many experiments can be registered to a single project; many subject groups can be registered to a single experiment, etc. A unique ID is assigned to each of these tables that can be used to identify the appropriate record to which data should be added.


Once a microscopy product is registered, i.e., an accession number is assigned, more detailed information may be supplied for specimen preparation, light and electron microscopic imaging, reconstruction and segmentation using the detailed data forms .

Step 1: Registering a Microscopy Product :

•  Log into the Telescience Portal - the following screen should be visible:


2. Select Register Microscopy Product. The Project Input Form should be visible.

3.  Each project is assigned a unique Project ID of the form P#### .

a.  Creating a new project: If a project ID has not yet been assigned, select the Create My Own Project button at the bottom of the form.

  i. Fill in the project details in the relevant fields. Definitions of fields can be viewed here (link to field definitions). Any fields designated by an * are required. If no information is available and the field in not required, leave it blank.

 ii. Once the details have been filled, click on the Use this Project button at the bottom left.

b.  Add to an existing project : To add a microscopy product to an existing project, select the project ID from the Choose menu or type in the project number in the box at the top of the form. To search for an existing project ID, use the Simple Project Search on the right hand side of the portal. Enter the search term(s) in the Look Up Project field. A list of matching projects will be returned. More detailed information can be viewed by clicking on the Details button. Details will be returned in a window below the list.


Note on Adding Data to the CCDB : The CCDB is a powerful database system that will allow users to manage their data and share their data with colleagues and eventually the broader scientific community. When adding data to the CCDB, the user should keep in mind that the more detailed the information provided, the more powerful the system will be. Towards this end, users should avoid meaningless or minimal information for projects and experiments and try to fill in as many fields as possible for each dataset. A list of definitions for each field in the CCDB can be found here (provide link). For example, using the word "tomo" in place of "tomography" for a project description will lead to difficulty searching and decreased value of the data record for anyone but the data depositor. Adding experiment names like "Experiment 1" or a purpose such as "test tomo" will also not be useful because it doesn't provide any meaningful information for subsequent search and gives no indication of what the experiment was designed to do. A few minutes spent now will save countless hours of frustration and countless dollars in wasted time and supplies later on.


3. Once the Project ID has been selected, click on the "Get Project Details" button on the upper right of the project form window. The details will be displayed in the main window. Users may edit details by selecting the Edit Project button at the lower right of the project window.


4. If this is the correct project, click on the Use this Project button in the lower navigation bar.


5. Create or add to an Experiment: Once the Use this Project button is clicked, the experiment table will appear. Just as with project, either select an existing experiment by using the "Choose" pull down menu or create a new experiment. Repeat this process through the existing 8 forms until the Microscopy Product form is reached. In each table, required fields are indicated by an *.

Navigate Function : The CCDB has created a "Navigate" function to allow users to provide an overview of data present in a given project and to make the process of adding records to an existing project faster and easier. Clicking on the Navigate button on the bottom menu bar will display a Project Summary in the form of a simple hierarchy. The summary displays the ID's of all records registered to a given project with a limited set of descriptive data to allow users to understand the record. The "children" of each record are displayed as a set of indented boxes. In the example shown below, subject 19 (mus musculus) belongs to Subject Group 14 (wildtype/control). Clicking on any of the boxes will display the detailed record for that item. Once a record is selected, users may add to it as described above.



Once the microscopy product table has been completed, users should make note of the ID supplied for the microscopy project. This identifier will be required for subsequent data entry. The CCDB assumes that a user is collecting a set of 2D images that are related in some systematic way: e.g., a series of tilt images that are obtained as a user is tilting a specimen in the electron microscopy or a time series. The microscopy product type field refers to the type of series that is acquired. Possible values include:

•  single axis tilt series ; images collected as the specimen is rotated around a fixed tilt axis

•  double axis tilt series : images acquired around a single tilt axis followed by rotation of the specimen and collection of a second tilt series.

•  Mosaic : images collected as a specimen is scanned systematically across the X and Y extents which will be knit together into a larger image

•  Optical section series : a series of images that is obtained through the depth of a section through optical sectioning, i.e., with a confocal or multiphoton microscopy, where out of focus light is eliminated from the focal plane

•  Through focus series : a series of images that is obtained through the depth of a section but without the removal of out of focus light

•  Time series : a series of images that are obtained at different time intervals

•  Serial section s: a series of consecutive sections that are cut through the thickness of the specimen

•  Stereopairs : a set of images obtained through a limited tilt range, meant to be viewed under a stereoscopic viewer

•  Survey sections : a set of images that isn't related in any systematic way but which were all obtained by surveying a specimen in a single microscope session

A given microscopy product may be more than one of the above, e.g., an optical section series mosaic.

Detailed Data Input/Uploading Files into the CCDB

Once this registration process is completed, users may add imaging, detailed specimen preparation, reconstruction and segmentation details to a given microscopy product. These details may be added in the same session, or in a later session. The basic workflow that is modeled in the CCDB is as follows:

Microscopy Product --> Raw digital data (Image 2D) --> Reconstruction --> Segmentation

Just as with the Project tables, this workflow is hierarchical where each top level can have multiple children, e.g., each microscopy product can have multiple raw digital datasets and each reconstruction can have multiple segmentations. However, unlike the first 8 tables, each of these main categories has additional branches that contain additional forms for detailed information. Thus, data input in this section isn't presented to the user as a simple set of linear forms. The forms in these sections also allow the user to upload data files and display images to the CCDB.

Step 1 :

•  Select "Detailed Data Forms" from the upper menu


2) Select the project ID from the list provided. Once selected, click the Next button at the bottom of the page.


3) Select the Microscopy Product ID from the list provided. Click Next . Once you've opened a session with a particular microscopy product, the product is considered checked out . Only one person can work on a microscopy product at a given time. If the product has been previously checked out by you, a check mark will appear next to the MPID. If it has been checked out by someone else, then an "X" will appear.

4) The information entered for the Microscopy Product form will be displayed in the main window. Additional forms for recording details for this microscopy product are shown in the side bar navigation on the left. Before proceeding, make sure that the correct Project ID and Microscopy Product ID are selected. The input forms are split into 5 sections:

a) Specimen Preparation : Detailed information about how the specimen was prepared for imaging.

b)  Microscopy Product information :

  i. Microscopy Product Type: details about specific product type, e.g., tilt series

  ii. Specimen information: anatomical details about the images acquired

  iii. Imaging parameters: details about the conditions under which the images were acquired

c) Image 2D Data : information about digital 2D images used for the reconstruction, including actual data files related to the raw images

d) Reconstruction Data : information related to the process of reconstruction from the raw data, including the actual reconstruction files and images

e) Segmentation and Analysis : Information about segmentation or quantitative analysis derived from the reconstruction, including the segmentation files and images


5)  Add Image product details by selecting the Imaging Product Info link from the left navigation bar. This form may also be accessed by selecting Microscopy Product Info and clicking on the Next button at the bottom. Click on the "X" in front of the appropriate product type. A custom form for that particular product type will be displayed. Once the form is filled out, click Save. Users may select as many of the different product types as apply to the data set. Once the session is saved, the "X" will be replaced by a check mark .

6)  Add Specimen Description information by clicking on the Specimen Description link on the left navigation bar. This form allows the user to provide an anatomical description of the data set, down to the level of subcellular structure (Structure). Note that for the subregion level, users may enter as many values as appropriate, separated by commas, to characterize the location accurately, e.g., area CA1, stratum radiatum. Users are also encouraged to submit an atlas map showing the location of a given dataset in a larger context, e.g., a brain atlas.

7) Add Imaging Parameters by selecting the Imaging Parameters link from the left navigation bar. Select either electron microscopy or light microscopy from the selection menu. The appropriate set of forms will be returned.

For light microscopy , once general information about imaging conditions is provided, select either Transmitted or Fluorescent details using the selection boxes on the bottom menu, then click Save . If Fluorescent is selected, choose from confocal , multiphoton or epifluorescence to view the correct forms for each of these types of microscopy

Saving/editing data

For the detailed information forms, data is not stored automatically in a permanent database, unlike the Basic Data Input Form. Rather, data is stored in a temporary location until the process of data entry has been completed and the data approved for submission to the CCDB. Users may save these temporary sessions, log out of the portal and then restore the session for adding more data or editing existing data. After filling out a particular form, users should click on the Add to Session button at the bottom of the page. This action adds the entered data to the active session, but DOES NOT save the session itself. In order to save the session for future use, users must click on the Save this Session button on the left navigation menu.

Note: Failure to click SAVE THIS SESSION before logging out will result in loss of information!!!

Users should click on Save this Session often during a data entry session to ensure that information is not lost. Information on Restoring a Session will be detailed in a later section.

STEP 2: Adding data files to the CCDB

Image 2D :

The Image 2D form captures details about the actual images used for reconstruction, along with snapshots of the 2D dataset for display on the web and a pointer to the full resolution data. A separate record may be created for every image in a dataset, e.g., every tilt image can have its own record. In practice, if the data are input manually, creating a separate record for each image is tedious. Rather, users should create a tar or zip file containing all of the images in a data set and provide summary information about the set. The number of images in a particular set can be entered in the Number of images in the data set field.

Some of the fields in Image 2D are duplicated from the Microscopy Product form because often the images are downsampled or cropped compared to the original images taken from the microscope. If the image 2D set has been digitized from negatives, information about the digitizing should be provided in the appropriate fields.


Uploading files to CCDB

The image 2D form is the first place that users will upload full resolution data to the CCDB. The CCDB does not store the full resolution data in the database itself, but rather stores a pointer to the data on CCDB's file system. In order to provide some idea of what is contained in the file, however, the CCDB stores a thumbnail and a 512 x 512 display image for viewing in a web browser. A higher resolution 2D image may also be placed on the Neuroinformatica image server for interactive viewing.

Loading images to the Neuroinformatica server will be covered in a separate section. Uploading data files and images to the CCDB, regardless of which form is active, always involves the same steps:


•  Click on the Upload File link. Whenever the user sees an Upload File prompt in the input form, the CCDB will launch a Java Webstart â application that will upload the file and store it in the correct location in the database.

•  Select a file from the local file system by clicking on the Open File icon in the Choose file(s) to upload window. Once the file(s) are selected, click on the OK button. A message will be displayed when the files have been successfully loaded. Files may be removed from the list by selecting the file icon with the red X through it.

Helpful hint: If the browser does not automatically the Java Webstart application, check the downloads for the getUploadJNLP.jnlp file and double click on the file name. This action should launch the application if the computer is configured to allow Webstart applications. For MacIntosh users: if the application doesn't launch, try adding a . jnlp to as the file extension before double clicking. Do not reuse old .jnlp files because they are specialized for loading data into a particular table of the CCDB.


Helpful hint : For very large files or if using a slow connection e.g., a cable modem, it is a good idea to save the session once the process of uploading has begun. Once the upload application has begun and a session is saved, the user may log out without losing data. If the session is not saved, the web application may time out before the upload is completed, and data can be lost.

Although multiple files can be uploaded at once, generally the CCDB is expecting a single file name per field. Therefore, only those files that meet the criterion of the field should be loaded when using this utility. If multiple files are to be uploaded for a given field, please tar or zip them into a single file.

For the Image 2D, Reconstruction and Segmented Object forms, the CCDB is expecting four types of files to be loaded and a description of each:

•  Downloadable data file : This file should contain the set of original data files in a .zip or .tar archive. This file is generally very large. See note above about loading large files into the CCDB. The file description should include a list of what exactly is in the tar file, e.g., "Tar file containing full size tilt images in Suprim format along with the fiducial mark files generated by IMOD." The more information that is provided, the more useful the data will be to future users.

•  Display image for Website : This image should be a representative image a particular type of data for display on the CCDB website, e.g., a single tilt image, a projection of a 3D data set or a single computed slice. The actual image may vary for each type of data and each data set. This image should be chosen so as to give a user an idea of what to expect with the full resolution data and should be 512 X 512 in dimension and in .jpeg or .tiff format. Annotations may be added to the image. It is also a good idea to add a copyright notice because these images will be available through the web once the data are released to the public. The file description should be geared towards a naïve user who is interested in learning about this data, e.g., "Maximum intensity projection of a selectively stained Purkinje neuron from the rat cerebellum."

•  Display Thumbnail : This image is a 100 X 100 version of the Display Image that will be used for quickly browsing through the types of data stored on CCDB. In the future, the production of the thumbnail from the representative image will be handled automatically. No description is required for this image.

 
Animation File : This file is an animation file that is meant to be viewable through the web. In general, this file should not be extremely large as this will take a long time to view. The file should be in Quicktime, MPEG or AVI format. Higher resolution versions of the animations may be included in the .zip/.tar file for the respective data type and made available for download.

Once the files have been uploaded and the session saved, the Upload file will be change to Replace uploaded file to indicate that a file has already been loaded. In the case of the downloadable file, the name of the uploaded file will appear. In the case of the display image files, a View uploaded file link will appear in the window. Clicking on this link will open a new window with the image displayed. If the image is not correct, the file may be replaced by clicking on the Replace uploaded file link.

For very large images (> 1024 X 10224), users may choose to provide on-line navigation capabilities through the use of the Neuroinformatica image server. The CCDB can provide a link to this server so that users may browse, pan and zoom on large images without having to download the image first. If the image is < 100 Mb in size, then click on the Launch button next to the Neuroinformatica link and follow the instructions for uploading the image. Once a link has been provided, cut and paste this link into the Neuroinformatica field in the Image 2D or Reconstruction forms.


Restoring a Session

Once a session is saved, it can be restored by selecting the Detailed Data Input Form tab in the top navigation bar. A list of currently saved sessions are provided at the top of the form. Select the appropriate microscopy product idea and click on Retrieve .

The status of the current saved sessions will be indicated in the Status column. Not submitted means that the session has been saved, but the data have not yet been submitted to the database. Once the record is complete, click on Submit for Approval , to let the curator know that the record is ready for entry. Once the curator has approved the data, it will be submitted to the CCDB. At this point, the user will no longer be able to edit the record without the permission and assistance of the curator and the database administrator.


Reconstruction

After details about the 2D images are recorded, select the Reconstruction link on the left navigation bar.

A list of current reconstructions entered for that microscopy product will be presented. In a future version, users may add multiple reconstructions to a given microscopy product but this function is not enabled at this time. To add a new reconstruction, select the New reconstruction button. The reconstruction form should appear. Only part of the form is shown in the above image. This form contains details about the reconstruction process and allows the user to upload data files, display images and animations. A detailed explanation of data/image upload is provided in the previous section. The information on volume dimensions and voxel scale is repeated because the volume may be subsampled or cropped compared to the 2D images used for the reconstruction.


Segmentation and Analysis


The segmentation and analysis forms record information about how the reconstruction was segmented and also the data files and display images for the segmentation. To add a new segmentation to an existing reconstruction, click on the Segmentation and Analysis link in the side navigation bar. This link will only become active once a reconstruction has been entered. The CCDB stores each object segmented from a reconstruction as a separate record in the database. Each object may be stored along with measured properties such as length, volume, surface area, image intensity, etc. To create the appropriate number of records, users should enter the total number of objects segmented from the reconstruction in the How many objects? box.

Once the number of objects is entered, the following form is provided:

The first part of the form is used to store general information about the segmentation and analysis procedure.

•  Segmentation person's name : The name of the person who performed the segmentation

•  Segmented object description : A general description of the method and rationale used to obtain the segmentation. Descriptions of individual objects are included in a different section.

•  Analysis description: Details about any procedures for preparing the volume for segmentation, e.g., filtering and thresholding for isosurfacing, or for obtaining measurements from the segmented objects, e.g., "Surface areas and volumes were calculated using Analyze 7.5".

•  Algorithm used for segmentation: Any general class or specific algorithm for generating automated or semi-automated segmentation, e.g., Level Sets, Watershed algorithm. Details should be provided in the Analysis description field.

•  Is this a manual segmentation : Indicates whether the segmentation was performed by manual tracing of 2D slices or painting of voxels.

 
Analysis file : Allows the user to upload an Excel spreadsheet with information on the individual segmented objects rather than filling out the on-line form. Clicking on the template link will download the Excel form that should be used.


CCDB has special parsers for neuronal tree structures that have been generated using the program Neurolucida (Microbrightfield , VT USA ). Neurolucida generates a set of text files containing quantitative information about the tree structures generated. These may be uploaded directly into the CCDB using the appropriate links.

As with the Image 2D and Reconstruction forms, users are able to upload the data files and display images for any segmented objects. See the instructions provided for the Image 2D section for uploading data files and images. Currently, no animated files are stored with the segmentation section, although this function will be added at a future date.

Users may provide descriptions and quantitative information about segmented objects either by using the Excel spreadsheet (see above) or by entering this information through the user input forms. CCDB generates a form for the number of objects specified by the user in response to the How many objects? box at the beginning of the segmented objects table (see above).

In the example given below, a form for 4 segmented objects was created:


The following information may be provided for each object:

•  Object Name: This field provides the name given to the segmented object by the segmenter. It should be the same as the name given in any segmentation file.

•  Object Type: This field describes the form of the segmented object. Acceptable values are:

•  Contour: object was defined as a set of 2D contours without further surfacing

•  Surface: Object was defined as a 3D mesh

•  Volume: Object was defined as a set of voxels

•  Tree: Object was defined as a branching tree structure, e.g., a model neuronal dendrite generated by Neurolucida.

•  Description : This field provides a description of the segmented object itself . The description should be intelligible to another human being, i.e., no abbreviations or non-standard usage. In the future, this field will be tied to a formalized ontology or other terminological resource.

•  # of objects : This field describes the number of separate sub-objects that may have been segmented as a group, e.g., multiple spines that are all included under the same object name.

•  Surface Area : surface area of the object in µm 2

•  Length : Length of the object in µm

•  Volume : Volume of the object in µm 3

•  Labeling Intensity : Voxel gray scale intensity measurement; generally used for protein labeling experiments

•  Labeling Rank : Relative measurement of labeling intensity within a single reconstruction.

•  Threshold: Stores the threshold that was used to define an isosurface or subvolume.

Downloading Files from the CCDB

Full resolution data files of all of the data contained in the CCDB are available for download. Users must agree to abide by the data sharing policies of the CCDB by agreeing to the terms of the licensing agreement. These terms require proper attribution of the data contributor and the CCDB when using the data for non-commercial purposes. Downloading data from the CCDB requires the following steps:

1) Select datasets to be downloaded using the check boxes on the Summary Search Results page

2) Select Add to MyLabBench and click Go.

3) Provide a valid e-mail address, name and institution. This information is required to track dissemination of data sets and also to allow the CCDB to provide users with updates to selected data. While the CCDB strives to correct all errors prior to upload, such errors are an inevitable part of human activities. CCDB will post updates to datasets and inform those who have requested the data. This information will not be required for users who have an account in MyCCDB.

4) Read and accept the conditions for download by clicking on the Accept and proceed to downloading.

5) If additional searches are required, click Back to Search Results in the Current Session box on the lower left panel. CCDB saves current session information so that users may continue to perform searches and selections. MyLabBench will be updated with the new selections every time a user adds to MyLabBench.

6) Review the datasets in MyLabBench for download. Data sets may be removed from the queue by selecting Remove. All data may be removed by clicking on Clear MyLabBench.

7) You may download all datasets in your lab bench by selecting the here button at the bottom of the page.

8) Click Download and the downloading utility will open as a Java Webstart application.

9) A description of all of the types of files stored for each dataset is found in the CCDB Data section. Many of the data files stored in CCDB are quite large so the download may take a few minutes. If the files are too large, or too many are selected, it is possible that the operation will time out. In this case, reduce the number of files selected or send a request to the CCDB. Anytime difficulty is encountered, the CCDB will be happy to provide the data on disk

Typers of Data Files in the CCDB

Main Image Files
For each data set, the contributors store the image data along with any ancillary files required to view or interpret the data. These types of ancillary files may include fiducial mark files, header files, etc. In the current version of the CCDB, the imaging and related files are bundled into tar files so that they can be retrieved as a single file. Image data may be compressed prior to creating the tar file, although storage of uncompressed raw data is encouraged. A description of the content of the tar file and any compression used should be included in the CCDB. For the formats and procedures used at NCMIR, the following tar files should be prepared:

Raw image data: A single tar or zip file should be prepared with the raw image data, that is, the imaging data that was taken directly from the microscope or digitized from negatives. Any files that are applied to the raw data for subsequent reconstructions, e.g., fiducial mark files, may also be stored in this tar file. Both the unaligned images and the cropped, aligned images may be included. If the cropping coordinates are stored in the CCDB, it is not necessary to store the cropped files. The user should be able to recreate the reconstruction from the raw data using the information provided by the CCDB and the image data provided. The file should be named: basename_img.tar.
The filename is stored in the image_filename field of the image2d_objtab

Volume data: A single tar file should be prepared with all 3D volume data. For Analyze files, the tar file should include the .img and .hdr files. The tar file may also include any volumes derived from the original which are deemed useful, e.g., filtered volumes. If additional segmentation was performed on the volume, the volume file that was segmented should be included and identified. The file should be named: basename_vol.tar.
The filename is stored in the volumename field of the reconstruction3d_objtab

Segmented data: A single tar file should be prepared of all segmented data. For Synu data prepared from Xvoxtrace files, this file should include the Xvoxtrace trace file, all synu objects created from this file and the Viewdata file. The file should be named: basename_seg.tar.
The filename is stored in the seg_filename field of the segmentedobject_objtab

Representative Images
In order to provide visualization of the content of a data set on the web, the CCDB offers low resolution 2D images for browsing, without the need for downloading data. At this time, users have to provide these types of images along with the full resolution 3D data. The CCDB has adopted standard sizes and naming conventions for these images. For each reconstruction stored in the CCDB, the user should prepare the following:

Raw Image Thumbnail: A 2D image representing the raw imaging data used to create the reconstruction, e.g., a single tilt image. The maximum dimension should be 512 and the format should be jpeg. The image should be named: basename_img.jpg.

Reconstruction Thumbnail: A 2D image representing the 3D volume. This image may be a single slice through a volume or a projection through the volume, whichever is deemed by the user to be more informative. The maximum dimension of this image should be 512 and the format should be jpeg. A brief description of the image which will be displayed when the image is selected should also be prepared. The image should be named: basename_vol.jpg. The description of the image is stored in reconimage_desc of the reconstructionimages_objtab. The filename is stored in recon_filename of the reconstructionimages_objtab

Segmented Object Thumbnail: A 2D image representing the segmented image. This image may be annotated, i.e., have labels placed on it identifying objects segmented from the reconstruction. The maximum dimension of this image should be 512 and the format should be jpeg. A brief description of the image which will be displayed when the image is selected should also be prepared. The image should be named: basename_seg.jpg. The description of the image is stored in seg_desc of the reconstructionimages_objtab. The filename is stored in seg_filename of the reconstructionimages_objtab

Animation or Movie Files
Animation or movie files may also be stored for each reconstruction for viewing on the web. These types of files are useful for viewing and evaluating 3D volume or segmentation data and may include the following:

Raw data Animation: Animation of an aligned dataset prior to further processing, e.g., single tilt series for electron tomography. A brief description should also be prepared. The movie loop should be prepared in mpeg or Quicktime format and should be of a reasonable size so that it will display with average bandwidth. The description of the image is stored in animation_desc of the animation_objtab. The filename is stored in animation_filename of the animation_objtab

Reconstruction Animation: A movie loop of the volume data. This loop may display the reconstructed object rotating along a single axis or may display the individual slices of the volume. Again, the user should provide whatever would be most useful to someone trying to evaluate the data prior to downloading it. A brief description should also be prepared. The movie loop should be prepared in mpeg or Quicktime format and should be of a reasonable size so that it will display with average bandwidth. The description of the image is stored in animation_desc of the animation_objtab. The filename is stored in animation_filename of the animation_objtab

Segmented Object Animation: A movie loop through the slices of the aligned and cropped imaging data used to create the reconstruction. The movie should be in mpeg format and no larger than 10 megabytes. The movie should be named: basename_img.mpg. The description of the image is stored in animation_desc of the animation_objtab. The filename is stored in animation_filename of the animation_objtab.

Users may also choose to make available other 2D images and movie loops relating to the raw data, volume or segmented data, but they are not required. If such images are created, they should adhere to the size requirements and naming conventions described above.