Using the CCDB with the Whole Brain Catalog
From Whole Brain Catalog
[edit] Upload Your Data Into the CCDB with the Whole Brain Catalog
You can simultaneously input data into the WBC and CCDB by using the Import File tool, which is the icon at the top left that looks like this: 
Upon clicking on this icon, the WBC will launch the CCDB data upload tool. When this window comes up, you should be already on the tab that says "Create Microscopy Registration" as shown:
While not all fields are mandatory, they should all be filled out as best as possible.
If the information is not available, fields can be filled in with "n/a". The fields correspond as follows:
Experiment Title - The title of the experiment
Experimenter - Who performed the experiment/project leader
Species - The species of animal used, eg. mouse, rat, human, etc.
Scientific Name - The scientific name of the animal used
Strain - The strain of animal used
Age Class - Age class of animal used (juvenile, adult, etc.)
Gender - Gender of the animal used
Microscope Type - Type of microscope used
Imagebase Name - Basename for the image used. For example, if you have files myfile1.jpg, myfile1.txt, myfile1.obj, the basename is myfile1
Product Type - Microscopy technique/product used
Instrument - Instrument used for experiment
When finished, click on the Submit button at the bottom of the page. A window will pop up informing you a new Microscopy ID (MPID) has been created. Take note of this number for future use.
[edit] Detailed Data Input
Next, click on the Detailed Data Input tab at the top. The Update Microscopy Registration tab can be ignored for now and is only used if you need to come back at a later time to update your original MPID registration data.
Once at the Detailed Data Input tab, you will see a series of MPIDs, projects, and images, along with a series of boxes that say upload and edit. Scroll to the bottom of the page and locate your MPID. Click on the edit box at the far right of your MPID. You will now be taken to the edit panel for your MPID. To ensure you have clicked on the correct MPID, ensure your MPID matches the one displayed on the second row of tabs from the top. In order to see everything, you may have to expand the window to a larger size. Your page should look like this:
While not all fields are mandatory, they should all be filled out as best as possible. If the information is not available, fields can be filled in with n/a. The fields correspond as follows:
We will start of the Image2D tab. This will be for all of your RAW data.
Number of Images - Number of images used for your reconstruction, or 1 if only single images are used for this dataset
X, Y, Z Size - X, Y, and Z sizes of the RAW data in pixels.
X, Y, Z resolution - X, Y, and Z resolutions of RAW data in um/pixel
Notes - Any additional notes that are applicable to the RAW data. For example, if raw data is manipulated before being stitched together for the final product, this is the place to mention that
When finished, be sure to click on the Submit button at the bottom of the window. DO NOT MOVE ON UNTIL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup.
If your raw data has gone through any reconstruction processes, we will then move on to the Reconstruction tab.
The fields correspond as follows:
Reconstruction Type - Type of reconstruction used
Reconstruction Program - Program used to perform the reconstruction
Reconstruction Algorithm - Algorithm used for the reconstruction, if any
X, Y, Z Volume Dimensions - X, Y, and Z sizes of the reconstruction in pixels
X, Y, Z Voxel Scale - X, Y, and Z resolutions of the reconstruction in um/pixel
Notes - Any additional notes that are applicable to the RECONSTRUCTION data. For example, if any additional steps or programs were used for this reconstruction, this is the place to mention that
When finished, be sure to click on the Submit button at the bottom of the window. DO NOT MOVE ON UNTIL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup.
If you have segmented any of your data, we will then move on to the Segmentation tab.
The fields correspond as follows:
Segmentation Person's Name - Name of the person who segmented the data
Segmented Object Description - Description of the segmented object
Analysis Description - Descriptions of the steps used to analyze and segment a reconstruction
Notes - Any additional notes that are applicable to the SEGMENTED data.
When finished, be sure to click on the Submit button at the bottom of the window. DO NOT MOVE ON UNTIL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup.
Next, we will move on to the Specemin Description tab. This is necessary for ALL datasets. The fields correspond as follows:
System - System the sample comes from
Tissue - Type of tissue from which the image is taken
Organ - Organ the sample is taken form
Region - Region of the organ used
Cell Type - Cell type examined
Cell ID - ID number given to the particular examined cell
Structure - Type of subcellular structure examined
Atlas Coordinates - Atlas used
Medial/Lateral, Dorsal/Ventral, Anterior/Posterior - Coordinates for each corresponding atlas plane
Notes - Any additional notes for the sample
When finished, be sure to click on the Submit button at the bottom of the window. DO NOT MOVE ON UNTIL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup.
Next, we will click on the Imaging Product Type tab, which works a little different than other tabs. Your window should look like this:
To use this page, you must first determine your image product type, which is noted at the top of each dark grey box in blue. Once you have determined your product type, click on the check box to the left of your product type's box. You may now edit the appropriate fields corresponding to your product type. When finished, be sure to click on the Submit button on the right hand side of the dark grey box for your product type. DO NOT MOVE ON UNTL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup. If multiple product types apply, you can check multiple boxes and fill out the appropriate fields.
Next, click on the Imaging Parameter tab.
This page works identically to the Imaging Product Type tab in that you must first select the appropriate box for your data before you can input text. There are two options: EM (Electron Microscopy) Product at the top, and LM (Light Microscopy) Product at the bottom. Click on the appropriate check box on the left for your corresponding product and fill in the appropriate fields. When finished, be sure to click on the Submit button on the right hand side of the dark grey box for your product type. DO NOT MOVE ON UNTL YOU HAVE CLICKED ON SUBMIT. This will be confirmed by a popup.
You should now be finished with all of the metadata for your particular MPID. If you want to go back and edit any of the data, you can always go back to any of the tabs you have previously entered data for.
After you are finished with inputting your MPID's metadata, you are now ready to upload your data. On the second row of tabs, click the home tab. You should be taken back to the list of MPIDs. For your MPID, click on the Upload Button on the right. The window should look like this:
For now, only one upload at a time is allowed, and only the image you want to display in the WBC. The following is accepted:
Images - png, gif, jpg (up to 2mb)
Neurons from NeuroML - .morph.xml, .nml (up to 2mb)
Mesh Models/Tomographic Segmentations - .obj (up to 5mb)
Images will be uploaded into either the Image 2D or Reconstruction tabs under Zoomify Image and Neurons or Mesh Models will be upload under Segmentation Data of the Segmentation tab. You will not be allowed to upload data for a particular tab unless you have already filled out the appropriate information from the previous section when you had clicked on edit.
To upload data, click on the Modify button for Zoomify Image under Image 2D and Reconstruction or Segmentation Data under Segmentation. Select the appropriate file and click on ok. Next, click on the upload button above the tabs and wait for the image to upload.
Upon completing this, close the Upload utility and the Upload Tool windows. You will now be back at the WBC. The program may seem to freeze for a moment, but this is actually the process of uploading your data. After a short while, the data you uploaded will appear on the screen before you with a wire box around it. You are now free to drag this box to its appropriate location within the brain.
