Page Comparison

STEP-0 Read instructions for logging specimens

STEP-1: Please pull up the Patient check list in BioMS using the Patient ID for which the protocol defines and accepts digital pathology images. For these 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 and as you can see, the Primary specimen, FFPE Tumor Block, is updated as “Not Collected” as a first step.

STEP-2: Click on the digital pathology specimen Upload icon. Alliance Digital Pathology Image Portal 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.

STEP-3: Read the instructions at the top of this page. For each digital pathology image file, you MUST enter the last two digits of the Surgical Pathology Number and Block ID. You must pick a valid stain type value from the drop down which contains all the commonly used stain types. Please note that the stain type values are sorted alphabetically and you need to choose the correct stain type for your image file. All the stain types currently available in the DPI Portal are listed at the bottom of this page as a link. 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_Last2Digitsof SPN_BlockID_Stain Type_.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 to add additional rows to add more files. In the example, below, user selected two files for upload. You may upload up to 15 digital pathology image files for a single patient. If you have a digital pathology image for which the stain type is not available in the dropdown of the DPI Portal, please email BioMS Help Desk at biomshelp@email.wustl.edu and request to add new stain types.

STEP-4: Once all the files are selected, then click Upload File, to initiate the file upload. Please note that you will have to leave the DPI window open while the file transfer is happening. The file transfer progress can be viewed on the screen as showed below. Please DO NOT close this tab while file transfer is in progress.

STEP-5: Once all the files have been successfully uploaded, you will see a completion message as shown below. At this point, you can close the tab and get back in BioMS to mark the Digital Pathology Image(s) as collected and then complete the shipment to the repository as usual. You will also receive an email with the same instructions to complete the collection and shipment in BioMS. For your convenience, a direct link to the Patient Checklist is included on the DPI Portal as shown below. By simply clicking the BioMS Patient Checklist link, you can complete collection and shipment for the digital pathology image(s). Please make sure that you enter the correct number of files you uploaded against the specimen quantity in BioMS while completing the specimen collection. Also, you may click the Exit button on the DPI Portal to close the DPI window. If for some reason your file upload attempt fails, then you will have to repeat the process from step-1 thru Step-4.

STEP-6: Once you are back on the Patient Check list page in BioMS, please mark the specimen as collected with the correct quantity and date/time. In the example shown, there are two files uploaded and therefore the quantity is entered as 2. IMPORTANT: DO NOT LEAVE COLLECTED SPECIMEN QUANTITY AS ZERO. THAT IS JUST A DEFAULT VALUE. Once you have completed collection, then you can proceed to Shipments as usual using the BioMS shipment workflow.

IMPORTANT: Depending upon your internet connection speed, the time taken for file upload will vary. We recommend using a computer with a wired internet connection rather than using a wireless internet connection to optimize and minimize the time taken for file uploads. If for some reason, you have a slow connection, the process will try its best to do multi part transfer and optimize the upload process but it may take some time. During this time, you can minimize the DPI window and continue to work on other tasks. As long as you don’t close the DPI window, the process will complete successfully. Also, please note that the DPI Portal is only meant for Digital Pathology Images and you should continue to upload deidentified Surgical Pathology Report for these digital pathology images directly in BioMS as you have done before.