18 - Digital Pathology Image Portal

IMPORTANT: Depending upon your internet connection speed, the time taken for digital file upload will vary. We strongly recommend using a computer with a wired internet connection to optimize and minimize the time taken for file uploads. While the file upload is in progress, you can minimize the DPIP window and continue to work on other tasks. As long as you don’t close the DPIP window, the process will complete successfully. For Digital Specimens, the Surgical Pathology Report (SPR) must be uploaded through DPIP and previously uploaded SPR thru BioMS does not meet this requirement.

STEP-1: Access the Patient check list in BioMS using the Patient ID:

Read the instructions for logging specimens. For the digital specimens, an icon, as highlighted below, will be shown next to the Specimen Actions. In the example shown below, the Digital Pathology Image is shown as an alternate to the Stained Slide - H/E and the Primary specimen needs to be updated as “Not Collected” as a first step and then, the alternate specimen “Scanned Slide Image-H/E” becomes enabled. You can review the detailed guide here on how to collect alternate specimens.

NOTE: In this example, Digital Specimen , “Scanned Slide Image - H/E” is defined with H/E as the expected stain type. However, it is possible that studies may allow digital specimens with any stain and in that scenario, the Specimen Comments Form becomes mandatory and User would have to enter the stain type under the Specimen Comments as shown in Specimen Comments screenshot below.

STEP-2: Access DPIP for SPR/Digital file submission.

Click on the digital pathology specimen Upload icon. Alliance DPIP will open on a new Browser tab. Please verify the Study ID, Patient ID and Collection Arm and Collection Event which are displayed at the top. A deidentified copy of the Surgical Pathology Report (SPR) that shows the institutional surgical pathology number and block ID, labeled with Alliance Patient ID number MUST be uploaded through the DPIP. This will facilitate rapid reconciliation between individual image files received and the corresponding slides described in the SPR, eliminating delays in confirming ‘acceptable’ submissions.

STEP-3: Select SPR for Upload:

Enter the Last 2 characters of Surgical Pathology Case# (SPN). Please note that only alphanumeric (alphabets and numbers) characters are allowed for the last 2 characters of SPN and no special characters are allowed. In this example, that value is “25”. Then click on Select Surgical Path Report to Upload SPR. The (Surgical Pathology Report) SPR file should be selected from your PC. Once the file is selected, DPIP will display its source file name as well as how it will be renamed using the standard file naming convention for SPR as follows: <<Study_PatientID_SPR_Last2SPN_DDHHMMSS>>. Also, once a file is selected for SPR, the checkbox stating that user previously uploaded SPR disappears. This is used for subsequent Digital Specimen File uploads if SPR was previously uploaded for the same Patient and the timepoint. For example, if there was an SPR already uploaded for the patient for one of the specimens under the same timepoint, the check box can be checked so that the user will not have to upload the SPR again for all the other specimens.

STEP-4: Select Digital Image file(s) for upload:

For each digital pathology image file, you MUST enter the last two characters of the Surgical Pathology Case Number (SPN) and Block ID. Please note that only alphabets and numbers are allowed for the last 2 characters of SPN and no special characters are allowed. You must pick a valid stain type value from the drop down which contains all the commonly used stain types. Each individual digital specimen file you upload must not exceed 5 GB (gigabytes) in size. Files larger than 5 GB cannot be uploaded. Please read instructions to understand how a SPR needs to be selected for upload first and then the Digital Images. Prior to uploading the file(s), please make sure to keep the source file(s) in a folder other than the “Downloads” Folder as local Endpoint Security Softwares might incorrectly interfere the file transfer process. The stain type values are sorted alphabetically based on its file extension values and you need to choose the correct stain type for your image file. All the stain types currently available in the DPIP are listed at the bottom of this page as a link. However, going forward, for most Digital Specimens in new Alliance Studies will be defined with specific stain type (H/E in this example) as shown and DPIP will only allow that stain type to be selected from the Stain Type dropdown. Once these are entered, click on the Choose File button to pick a file from your computer directory. Once the file is identified, click on it and then click open on the dialogue box to complete the selection. Based on the Alliance Digital Pathology Image standard naming convention (StudyID_PatientID_Last2CharsOf SPN_BlockID_Stain Type_DDHHMMSS_.svs), the file will be renamed and the revised file name as well as your original file name will be shown. You may click Add button to add additional rows to add more files. In the example, below, user selected three files for upload. You may upload up to 15 digital pathology image files for a single patient. If you have a digital pathology image defined without a specific stain value and you have a file for which the stain type is not available in the dropdown of the DPIP, please email BioMS Help Desk at biomshelp@email.wustl.edu and request to add new stain types. New stain type can be added once it is approved. You can review available stain types at List of Stain Types In this example, 3 Digital Specimens with H/E Stain Type are selected for upload.

STEP-5: Start File Upload process:

Once all the files are selected, click Upload File, to start the file upload. Please note that you will have to leave the DPIP window open while the file transfer is happening. The file transfer progress can be viewed on the screen as shown below. Please DO NOT close this tab while file transfer is in progress.

STEP-6: Keep the DPIP window open until file uploads are completed.

Once all of the files have been successfully uploaded, you will see a completion message on the DPIP screen as shown below. Now, you can close DPIP and get back to the Patient Checklist in BioMS to update collection details for the Digital Specimens. You will also receive an email (Subject: Digital Specimen and SPR file upload and Collection in BioMS) with the same instructions to complete the collection and auto shipment in BioMS. For your convenience, a direct link to the Patient Checklist is included on the DPIP screen as shown below. By clicking the BioMS Patient Checklist link, you can get back to Patient Checklist in BioMS.

Note: Make sure you complete steps for uploading SPR and Digital Files for ALL of the Digital Specimens you are planning to collect by repeating steps 1 thru 6.

STEP-7: Enter specimen collection data for ALL Digital Specimens on BioMS Patient Checklist:

Once you are back on the Patient Check list page in BioMS, please enter specimen collection details with the correct quantity and collection date/time from the SPR. In the example shown below, there are three digital specimen files with H/E stain are uploaded and therefore the quantity is entered as 3. Note that in this example, only one of the Digital Specimen (Scanned Slide Image - H/E) collection is shown. However, you need to make sure that DPIP process is completed and collection information is entered on BioMS Patient Checklist for ALL Digital Specimens you are planning to collect.

IMPORTANT: DO NOT LEAVE COLLECTED SPECIMEN QUANTITY AS ITS DEFAULT VALUE AND ENTER THE ACTUAL COLLECTED QUANTITY.

STEP-8: Save and Submit as final step

Once all collection details for all Digital Specimens are entered, Click on Save button at the bottom. Please DO NOT click save before completing the collection details for all Digital Specimens. BioMS will update the Digital Specimen as “In Transit” and will auto generate an electronic shipment. In near real time, BioMS Shipment Manifest will be auto generated and will be emailed to the submitting user and to the biorepository contact.

IMPORTANT: PLEASE MAKE SURE TO ENTER COLLECTION DETAILS FOR ALL DIGITAL SPECIMENS YOU ARE PLANNING TO COLLECT BEFORE CLICKING THE SAVE BUTTON. THIS IS IMPORTANT SO THAT ALL COLLECTED DIGITAL SPECIMENS CAN BE PLACED INTO A SINGLE ELECTRONIC SHIPMENT WHICH WILL MAKE REPOSITORY STAFF’S JOB EASY WHILE RECEIVING THE SHIPMENT/DIGITAL SPECIMENS.

Commonly Used Stain Types which are available to use in the DPIP can be found here: Stain Types available in Alliance DPIP

Please contact the BioMS help desk at: biomshelp@email.wustl.edu with any questions, problems, or suggestions with regard to using the DPIP tool.