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  1. How to acknowledge the use of images?
  2. How to create a collection?
  3. Can I declare my collection to be private?
  4. How to batch download images?
  5. How to add processed images to the database?
  6. CSV file format
  7. How to batch upload processed images?
  8. How to upload metadata for images in a collection?
  9. How to cite?

How to acknowledge the use of images?
All users of the cite are strongly encouraged to acknowledge the countless hours of work that has gone into the primary collection and preparation of images contained here. The long-term sustainability of this database depends on your support and acknowledgement via one (or more) of the following methods:

  • Cite both the primary reference associated with each image and the Cleared Leaf Image Database as part of any use of images contained in this site:

    Cleared Leaf Image Database, http://www.clearedleavesdb.org
  • Follow the license rules associated with each image.
  • Reach out to curators of images in cases where further collaboration is warranted.

How to create a collection?
To create a collection register at the site. To bulk upload images to the collection select "Image Curator" check box on the user registration form.
Select "Create Collection" link on the main menu and provide collection details.

Can I declare my collection to be private?
Yes. While creating a collection, select 'private' option in collection visibility section. To mark an existing collection to be 'private', select a collection from your 'Managed Collection' list, click on the edit tab and select 'private' option in collection visibility section.

How to batch download images?
Images in the user's managed list can be bulk downloaded as a 'zip' file with image metadata. Only a registered user can add images to the managed list and download from it. To add images to the managed list, search for images in the 'Search Images' page and select required images and click on 'Add to managed list' button. Images can also be added from the collection view page. Go to 'Managed Images' page and select images and click on the 'Download' button.

How to add processed images to the database?
A registered user can add processed images to the database. Processed images are associated to an image. You can add processed images in either of following ways:

  • From the image view page: Select an image from anywhere (Collection view page, image search page) in the site to go to the view page. Click on the 'Add new processed image' link to add processed image and it's results to the database.
  • Batch upload processed images and it's result file using our client application. You will need Java 6 (or later version) to run this application. Download java here. To run our application you will also need a file (csv) containing comma separated values of processed image details. Check CSV file format section for details. Download our application.

CSV file format
The CSV file required for batch upload of processed images is required in following format.
Parent Image Name, Parent Image Id, Processed Image File Name, Result File Name,Software Used, Brief Description about Processing.
eg. sample.jpg,1234,sample_processed.jpg,sample_processed_result.xls,LEAF GUI,Leaf vein extraction
Check this sample file. We encourage you to download images using batch download functionality and editing the downloaded csv file with image meta data.

How to batch upload processed images?
Download the application. Copy the application to the directory containing processed images and csv file. Open a command prompt/shell/terminal window. Go the directory containing application and processed images. Type the following command and hit button.

java -jar clid.jar sample.csv user_name password

Replace the following:
sample.csv with your file name
user_name with your database user id
password with your database password

How to upload metadata for images in a collection?
Download this sample excel file. Prepare an excel file (only .xls i.e. MS Excel 97-2003 workbook) or CSV file containing exact same number of columns seen in the sample file. We suggest, make a copy of the sample file and fill in the details for each image. Information in the first column i.e. image file name is required. Once you have a file ready, go to your collections list page by selecting "MY COLLECTIONS" sub-menu from the "COLLECTIONS" menu, select a collection, click on the "Upload Metadata" link on the collections view page. It will take you to a page to upload an excel file for the collection.

How to cite?
If you are using any image from this site, please cite this database in your work. Please include the following information:
1. Curator provided description of the image collection
2. Citation to our database: Das A, Bucksch A, Price CA, Weitz JS; ClearedLeavesDB: an online database of cleared plant leaf images.; Plant Methods 2014, 10:8.

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Cleared Leaf Image Database

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