This version applies to the current release of the BisQue user manual.


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For overview information about BisQue, see Bisque on the CyVerse website.

Bisque User Manual

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You can use the BisQue uploader to upload a file or image in any browser. You may also upload all the files in a directory in the Google Chrome browser.

To see which file formats are allowed, click at the top right of the Upload window. Unrecognized files will be uploaded as a file type; you can annotate the file textually and download the original at any time.

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Should you encounter a problem with any of the supported format types, please see Getting Help with BisQue. You may also want to read about file names for BisQue imports on Ask CyVerse.

BisQue allows zip and tar (BZ2, ZIP, and GZIP) compressed files. For more information on unrecognized files and compressed files, click Help at the top right of the Upload window.You also can upload large resources (tens of GBs) or automatically upload images from your microscope or camera using iCommands, and upload resources from 40-100 GB via a graphical interface using Cyberduck. For more information on other upload methods, see Manage Data on the CyVerse website.

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Be aware that the folder structure created in the CyVerse Data Store will not be visible in BisQue. Image files uploaded via iCommands or iDrop must be placed in the bisque_data folder to be visible in BisQue.

Once the items have been uploaded, you can store, visualize, analyze, compare, tag, and annotate them within BisQue, regardless of size or upload location.

Uploading using the BisQue uploader

Step 1: Open the Upload window

  1. Launch BisQue.
     How do I do it?

     Click Sign in at the top right of the window, click Sign in again, enter your CyVerse user name, and then click Login. If you haven't already done so, you will need to get access to BisQue. Learn more about logging in and out of BisQue at Logging In and Out of BisQue.

  2. Click Upload on the top toolbar:
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To view the list of supported image format types, whether the file has read or write capabilities, the file extensions for the file, and the source, as well as .zip and .tar files for multi-plane images or time-series images, click  at the top right of the window.

To sort on a column in a section or hide or show the columns that are displayed, hover over the column header and click , and then click the option to use.

Step 2: Change the upload folder

You can select a different upload folder, create a new folder, or delete a folder.

  1. Click .
  2. To select a different folder, click the folder to which you want to import the items.

    Uploading directories

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    Only upload to a directory under the home directory.

     

    • To create a new folder: Click Create, enter the folder name, and click OK.
    • To delete a folder (but not the files in it): Click the folder name in the list and click Delete.

Step 3: Create and edit the upload list

  • To select individual files:

    1. In any browser, click Choose files to select the files or images to upload.
    2. Select the files to upload and then click Open.
  • To upload all files in a selected folder (only in Google Chrome):
    1. In Google Chrome, click Choose directory.
    2. Select the directory with the files to upload and then click Upload.
      All files in the directory are added to the upload list.
  • To remove a file from the upload list, click to the right of the name in the list.

Step 4: Attach the files to a dataset

You can create a dataset in the Upload window or attach the files to an existing one. All uploaded files in the list must be attached to the same dataset. The options to add or use an existing dataset are available after you have created the upload list. You also can create a new dataset in the home screen.

For more information on using datasets, see Using Datasets.

  • To create a new dataset:
    1. Click Create a dataset at the bottom of the screen.
    2. Edit the dataset name as needed and click OK.
  • To add the files to an existing dataset:
    1. Click Add to existing dataset.
    2. In the Dataset browser window, click to select the dataset and then click Select.

Step 5: Change the permission level for each file (optional)

By default, uploaded items are set to private visibility, which means only you can access or view the file. You can change the permission setting for some or all files in the list.

For information on changing the permission level after the upload, see Changing Resource Visibility to Published or Private.

By default, files are uploaded as private visibility level, which means only you can access or view that element. You can change the visibility to public so everyone can use and view it. This can be done when you upload the element to the BisQue repository or after it's been uploaded.

  1. To change the permission for a file in the Upload list, either:
  • Click private to the right of the filename in the list to change the permission for the item to published.

–or–

  • Click published to change it back to private.

Step 6: Add metadata (annotations) to images

You can add, delete, and IR import metadata tags (annotations) to datasets or selected files now or later.

For information on adding metadata to files after the file has been imported, see Adding Graphical and Textual (Metadata) Annotations to Resources.

  1. Either:
    • To add metadata to all files in the dataset, click on the Annotations tab at the right.
    • To add metadata to a selected file in the dataset, click the file and then click .
  2. Double-click in the Name field, and either select a name from the drop-down list or enter a new metadata name.
  3. Double-click in or tab to the Type field and enter the metadata type.
  4. Click Update.

Step 7: Upload the list

When the list is complete, click Upload at the bottom of the screen.
The items are uploaded and may be accessed both in your My recent stuff list and in your list of files or images when you click Browse.

More about images

Want to learn how to rotate an image? See Rotating BisQue Images.

Helpful Links