Data Ingestion

1. Navigate to any folder in the Repository (click on the Repository button from the Navigation Menu 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

1. Navigate to any folder in the Repository (click on the Repository button from the Navigation Menu then navigate to a folder)

2. Click on the 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

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

2. Click on the Details button on the notification

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

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 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

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

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

2. Click on the Dismiss button on the notification

An MRXS image consists of a base .mrxs image, and a correspondingly named folder which contains:

• Slidedat.ini: Metadata for the entire image
• Index.dat: Index describing how the data files are combined into a WSI
• DataXXXX.dat: One or more image data files

Example: An archive file named "slide_001A.zip" containing:

slide_001A.mrxs
slide_001A/
    Data0000.dat
    Data0001.dat
    ...
    Data0021.dat
    Data0022.dat
    Index.dat
    Slidedat.ini

An AFI image consists of:

• IMAGE_NAME.afi: An XML manifest of the files representing each channel
• *.svs: One or more images, each representing a channel

Example: An archive file named "273481.zip" containing:

273481_Alexa Fluor 488.svs
273481_Alexa Fluor 594.svs
273481_DAPI.svs
273481.afi

An NDPIS image consists of:

• IMAGE_NAME.ndpis: An INI-like manifest of the files representing each channel
• *.ndpi: One or more images, each representing a channel

Example: An archive file named "Ex_changer.tar.gz" containing:

Ex_changer-DAPI.ndpi
Ex_changer-FITC.ndpi
Ex_changer-TxRed.ndpi
Ex_changer.ndpis

An image in the Lunaphore variant of OME-TIFF can have an auxiliary XML file which defines the minimum value, maximum value, gamma value, and pseudocolor for each channel. This XML file needs to match the filename of the OME-TIFF file with ".xml" appended.

Example: An archive file named "Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.tar" containing:

Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.ome.tiff
Lunaphore 10plex (5 cycles)_Slide 7_Annotation 1.ome.tiff.xml

A VSI image consists of a base .vsi image, and a folder named _IMAGE_NAME_ which can contain a variety of subfolders and files.

Example: An archive file named "Her2.tar" containing:

Her2.vsi
_Her2_/
    stack1/
        frame_t.ets
    stack10001/
        frame_t.ets
    stack10004/
        frame_t.ets