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Data Ingestion


There are several ways to upload images into the Repository. Depending on the desired workflow and volume of data to be ingested, use one of the following methods:

  • Upload files manually in a browser
  • Upload in bulk from a PC using the Upload Client software
  • Configure the image ingestion service by contacting support
  • Upload through the API for customized workflows

Manual Uploads

Files can be manually uploaded into a folder using drag and drop or through a file selection dialog. Multiple images can be selected for upload using either method. The status of uploaded files will be indicated through a progress notification at the top of the screen as well as a progress bar on each new item in the Folder Listing.

To upload file(s) using drag and drop

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Drag one or more files onto the folder listing area (until the “Drop files to upload” notification appears) then drop the files

  3. To check upload status, click on the Details button from the upload progress notification at the top of the screen

To upload file(s) using a file selection dialog

  1. Navigate to any folder in the Repository (click on the Folder Repository button from the left-hand sidebar then navigate to a folder)

  2. Click on the Actions button at the top right of the item list

  3. In the popup menu, click Upload

  4. Click in the blue box to activate the file selection dialog or simply drag files into the blue box; repeat as required for other files

  5. Click on the Start Upload button to start upload

  6. Click on the X button to minimize the File Uploads dialog

  7. To check upload status, click on the Details button from the upload progress notification at the top of the screen

To check the status of recently uploaded files

  1. Look for the upload progress notification at the top of the screen

  2. Click on the Details button on the notification

To edit metadata for recently uploaded files

  1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the Details button. If the notification has been dismissed, this method is not available and file metadata can be edited individually through the Repository listing

  2. Click on the Edit Metadata button for any of the files listed

  3. In the Add fields box look for the fields to be added or type a few letters to find the desired field; repeat as required for other fields

  4. Edit the value in the provided field

  5. Click on the Save Changes button to commit the field(s), or click on the Cancel button to discard changes

  6. Click on the X button in the top right hand corner of the File Uploads dialog

To locate recently uploaded files

  1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the Details button

  2. Click on the Folder button below any of the recently uploaded files

  3. Click on the X button in the top right hand corner of the File Uploads dialog

To clear the completed list of recently uploaded files

  1. Look for the upload progress notification at the top of the screen and, if it has not been dismissed, click on the Details button

  2. Click on the Clear Completed button

To clear the upload progress history and remove it from view

  1. Look for the upload progress notification at the top of the screen

  2. Click on the Dismiss button on the notification

Refreshing the page while uploads are in progress will terminate in progress uploads and clear the list of recently uploaded files.
Image formats that have multiple files per image (e.g. MRXS, VSI, AFI, NDPIS) must be packaged into a single archive file (e.g. tar) with the index files appearing at the root of the archive and all other related files and folders in the usual place relative to the index file. The system will automatically unpack these files after upload is complete.

Upload Client

Where the volume of images to be uploaded is large, it can be more efficient to upload images with a dedicated tool. The Upload Client is a Windows application that has been designed for automating image uploads. It can be configured to upload images that appear in a "watch" folder. Once the images are uploaded, they are available for review in the Uploads section of the application, from where they can be moved to the appropriate folder in the Repository.

The Upload Client can be configured to detect and upload images that are generated by a whole slide image scanner or it can be used to batch upload images on demand.

Contact Pathcore Support to access the upload client and learn more.

Indexing Service

[addon] [on-prem]

The indexing service has been designed for on-premise deployments. The service will find all the images in an attached storage system and reproduce the storage hierarchy in the Repository. The service provides a very efficient mechanism for managing storage in an on-premise deployment.

A side effect of the indexing service is the possibility in some circumstances for duplicate records to be created in the Repository. Images that are moved or copied on the storage system after they have been found by the indexing service will result in duplicate records, as the duplication will be detected by the service as a new file. This is not a huge problem, because both records will function normally (i.e. they will be viewable, no broken links, etc). However, the 2nd record won't have any of the annotations or metadata that may have been associated with the first record.

To reorganize the images in the Repository, we recommend using built-in copy or move functions, which handle image metadata. Note that copy operations in the Repository are shallow, so the image data will not be duplicated on disk.

Custom Built Uploader

Users can develop custom upload workflows using the API, which provides methods for adding files and metadata to the Repository. Contact Pathcore Support to learn more.