Bulk Uploading Image Files

The easiest way to add imaging data is via the web interface, using the method described in Submitting Specimen Data. If you have many files to upload, however, it may be more convenient to use the DERIVA bulk uploader tool.

If you’re not already familiar with the concepts and steps described in the Submitting Specimen Data page, please review them. The bulk upload tool is a replacement for *6. Upload Image Files** from that page.

Step 1: Create Specimen records

Create specimen records as described in Submitting Specimen Data.

Make sure you assign each record a unique Internal ID; the Internal ID is used to link image files with the corresponding Specimen records.

Step 2: Put images where the upload tool can find them

In order for the upload tool to find your image files, you’ll need to organize your files as follows:

For 2D files:

• Create a folder called deriva.
• Within deriva, create a folder called images
• Within images, save your image files, using filenames with the following naming convention:

{internal_id}-{number}.{suffix}

Where:

• {internal_id} is exactly the same as the Internal_ID value of the corresponding specimen
• {number} is a number; if you have a specimen with multiple images, this will control the order in which they’re displayed (if you only have one image per specimen, just use “1”).
• {suffix} is the suffix, indicating the file type (czi, jpeg, jpg, tif, etc.)
• Note that a hyphen (-) is used to separate the {internal_id} and the {number} in the image filename.

For example:

For 3D files:

• Create a folder called deriva.
• Within deriva, create a folder called image_3d
• Within image_3d, save your image files, using filenames with the following naming convention:

{internal_id}-{number}.{suffix}

Where:

• {internal_id} is exactly the same as the Internal ID value of the corresponding specimen.
• {number} is a number; if you have a specimen with multiple images, this will control the order in which they’re displayed (if you only have one image per specimen, just use “1”).
• {suffix} is the suffix, indicating the file type (czi, jpeg, jpg, tif, etc.)
• Note that a hyphen (-) is used to separate the {internal_id} and the {image-type} in the image filename.

Step 3: Upload the files

Follow these instructions to upload your file, pointing the uploader at the images subfolder.

Step 4: Fill in any missing data

Follow the instructions at Submitting Specimen Data to add anatomical sites, antibodies, etc.

Step 5: Update the curation status

Your new records will initially be marked “In Preparation” and will be visible only to consortium members. Change the Specimen records’ status to “Submitted” to forward them on to the Biocurator for review and release.