SCAUP - User guide

1. Enter in browser:
   https://ebic-scaup.diamond.ac.uk/
   Login/authenticate the usual way with your FedID and password.
    
2. Click on ‘List proposals’.
   Search and select your proposal.
   Click your session from the list of sessions.
   You will be then taken to the session page as shown below in the image:
    
3. Click on ‘Edit sample information’ (highlighted below in blue circle).
   
    
4. You will be taken to that session sample and shipping dashboard as shown below in the image:
   

5. Give a name to your shipment (Use a descriptive name, that indicates what the samples will be used in. For example, "FIB") under ‘Create New Sample Collection’. Click on Create (inside blue circle in the image in the tab section above).

5. (i). If you had already added some Samples and you are returning, then you can select them from ‘Select Existing Sample Collection’ – as shown in the blue circle in the below image:

Note:

You can edit your ‘existing sample collection’ until you have booked a shipment.
 

5. (ii). If you want to use an existing sample/s that is already at the facility (sent during a previous session), then give it a name, click on ‘Use Existing Samples’. It will take you to the page shown below. Type the session number, click Select. This will give you list of samples added for that session. Select the ones that you want for the current session and click, ‘save and continue’. Please see the screenshot below:

Note:

• You can only add samples from the same proposal.
• You cannot edit information on already existing samples. You can only view them.
• You can only transfer the samples once from one session to another.

If you are adding existing samples that are at eBIC then skip to section 14 (pre-session info.)

6. After clicking on ‘Create’ new sample (point 5), it will take you to sample information pages (screenshot below) where you will add samples, grids, grid boxes, containers and dewar information by following the steps and clicking continue at the end of each section.
   
   

7. Click on ‘save’ (highlighted in dark blue circle in the below image) after adding samples. Once saved it will be displayed in the overview section (right side of the page). Click on ‘Continue’ if you want to move to next section (light blue circle) or click on ‘Create New Item’ if you want to add more items (green circle) or click on any sample in the overview section to make changes, if required. Press ‘Save’ (dark blue).
   
   

Note:

1. You can create multiple copies of the same sample by simply adding the number of copies you want under ‘Copies’ (red arrow). They will be automatically assigned numerical suffixes starting from 1.
2. You can only select the sample that is under the ‘Macromolecule’ (red arrow) drop down menu. This is the sample that is part of your proposal in UAS.
3. Selected macromolecule will be added as a prefix to the samples.
4. Compulsory items are indicated with an Asterix mark. You have to select an option from the drop-down menus.  
   
   Once you are ready click on ‘Continue’. The next sections (‘Grid Boxes’, ‘Containers’ and ‘Dewars’ sections) follow a similar theme.

8. In the Grid Boxes section, please select type of grid box that best represents your grid box (the grid box schematic on right side changes based on the type you select). You can then click on the position in the grid box schematic and add samples from the previous section in the appropriate slots (red arrow in the screenshot below).

Note:

1.  Once a sample is added the grid box location changes to blue.
2. In the overview section, once added the samples will appear under the Grid Box section (red arrow) and the rest will be under unassigned section (grey arrow).

9. In the Container section, select puck or falcon tube. If it is puck then select the type. Now add the grid boxes from the previous section to the puck/falcon tube. See below screenshot.

Note:

1. In the overview section, once a grid box is added to the puck it will appear under the Puck section (red arrow).

10. In the Dewar section, if you have a registered dewar then select the correct dewar code (blue circle) that you are sending to eBIC for the current session. Click Add (red arrow) and select the container/s that you are sending. See below screenshot.

If you do not have a registered dewar code, you can ‘Generate a New Code’ by selecting it from the drop-down menu (blue circle in below image). This will generate a new dewar bar code and associate it with your proposal which you can use for you future sessions as well.

Note:

1. Do not generate a new dewar code when your dewar already has one on it. Use the existing one.
2. You will be able to print out your dewar code label (near future) along with the rest of the labels when you click on the ‘Print tracking label’ later (point 15).

11. Click on continue and it will take you to a sample review page of all the items you have added so far. This is a good point to go back and make any changes, if required.

Note:

1. Grids, Grid boxes, Pucks and Dewar are colour coded and can be collapsed or expanded in the overview section on the right-hand side. See arrows in below screenshot.

12. You can then proceed to the ‘pre-session info’ section. The information you added so far will be stored as a draft and will be displayed in the Scaup home page (inside the circle in the below image). You can modify a ‘Draft’ anytime until a shipment is booked at which point you cannot edit it anymore.

Note:

1. Depending upon the status of your shipment the information about your shipment will change from Draft to Submitted or Shipped or Returned (see red arrow below)

13. After you have added information about your grids, grid box/es, container/s, and dewar/s in their respective sections you can now proceed by clicking on ‘continue to pre-session info’ (highlighted inside blue circle below)

14. Pre-session information page (see below): Information from this section is necessary for proper grid loading and preparation of the electron microscope by the local contact. Please fill in all necessary details and any other relevant information in the section that says, ‘Any other information relevant to your session?’ Once you are done click ‘Finish’ (highlighted in blue circle below).

Note:

1. Grids for the session are expected to be either clipped or unclipped. Please select accordingly. If you have a mixture (which should not be the case), then please mention that in the ‘Any other information’ section.
2. While it is useful to mention it here you can also email your local contact with information that is relevant to your session such as collecting data in CDS mode, collecting un-binned super-resolution data, etc,…
3. If you have decided on a different collection scheme than what you have input in the pre-session info then please contact your local contact as soon as possible or before the start of your session.

15. The next page will give you a summary of the contents of your shipment (below screenshot). You can either continue to arrange the shipping (green circle) or go back (grey arrows) to view/edit the info that you added so far. You can even print the shipping labels in this page by clicking on ‘Print tracking labels’ (red arrow).

Note:

1. Clicking on ‘return to the sample collection summary’ will take you to the summary page as shown in point 19 and clicking on ‘return to sample collection list’ will take you to the session homepage as shown in point 5.
2. Before you proceed to arranging your shipment, please check that you are satisfied with the information that you provided about your session. Once you click on ‘Arrange Shipping’ your session sample details will be locked, and you will no longer be able to edit.
3. If you do not plan to use Diamond's own courier (DHL, on Diamond's account), you do not need to arrange shipping through Diamond. When using your own courier, ensure the labels provided by your courier are securely affixed (Red arrow in the above image).
4. If your shipment originates from outside the UK, and you plan to ship through Diamond, email eBIC support at ebicadmin@diamond.ac.uk (Blue arrow in the above image).
5. Please print tracking labels document and attach them to your shipment as per the instructions. An example of the tracking labels is below.

16. Clicking on ‘Arrange shipping’ will take you to a page (screenshot below) where you can add your contact details that are necessary for the courier of your dry shipper to eBIC. Make sure your address is correct. Click ‘Next’ once you are done adding contact details (dark blue circle).

Note:

1. When you login for the first time you will have to manually add this information. Thereafter, you can select from the existing saved contacts (in light blue circle).

17. Enter location and a convenient time slot for a courier pickup in the next page and click ‘Next’.

18. In the next page is a booking summary page with info which you added in the previous pages. Make sure it is correct, if not go back and modify. The courier shipping labels/waybill are generated and embedded in the page in pdf format. You can take a printout and paste it to the dry shipper before sending it to eBIC. This page will also have tracking details once your shipment is picked up.

Note:

1. Once your shipment is picked up you will also get the location updates under tracking details (light blue circle). Additionally, you can also get tracking and location details of your shipment when you click on ‘Manage Dewar Logistics’ in the Sample summary page (Refer to point 19).

19. Click ‘Done’. You will be then taken to the session summary page from where you can access sample info, pre-session info, manage dewar logistics and bookings and labels for that session (red arrows in the below image). This summary page has three main features: (a) Samples, (b) Cassette and (c) Actions

Note:

1. When you click on Manage Dewar Logistics you will be taken to a page where you can view the tracking history of the shipper and ask the shipper to be returned to your facility (refer to point 23 for dewar return process).

20. (a) Samples: This section, (within the black dotted lines in the below image) gives a list of all the sample grids added and/or imported for this session. There is information next to the sample about grid box location (red arrow). You can also view further details about the sample by clicking on View Sample (blue arrow). When you click on ‘Import Samples from Session’ (within blue circle in the image below) you can add samples from a previous session that are already at eBIC. Please refer to point 5(ii) for details on how to import samples.

Note:

1. ‘Import Samples from Session’ let’s you import samples from a previous eBIC session of the same proposal, for example, samples from a successful FIB-milling session can be imported to a tomography session.

21. (b) Cassette: This section (within the red dotted lines in the image below) is a representation of a cassette loaded in the microscope. The local contact for the session will map the sample grids (shown in sample section) to the cassette positions.

Note:

1. Only the local contact of the session has the permission to map grids to cassette locations. This is done by clicking on the cassette position in the Cassette section and selecting the appropriate sample from the list. Once mapped, loaded grids will be highlighted in blue while the empty ones will remain white.

(c) Actions: In this section (within blue dotted line in the image below), you can perform several tasks such as edit sample and pre-session info., book shipment and print labels, track dewar location and return your shipment. Additionally, you can get access to sample and session metadata information by printing them in pdf format (red arrows below). Examples of some metadata and pdf files are shown below.

Note:

1. Clicking on Print Contents will take you to printable pages that can be either opened in a mobile phone/tablet or printed before/after the session.

22. Accessing PATo from Scaup: Once data is collected and processed by the auto-processing pipeline, a ‘View Data’ button will appear for all samples whose data has been collected (highlighted in red circle in the image below). Clicking on ‘View Data’ will directly take you to the PATo page that displays the processing results for that sample.

23. You can ask for your dewar to be returned to you after the session from the summary page by clicking on ‘Manage Dewar Logistics’ (Highlighted by the light blue circle in the screenshot below). Click on Manage Dewar Logistics (within light blue circle in the above image) and then click on ‘Request return’ on the next page (screenshot below). You will be then re-directed to the old SyncWeb/ISPyB webpage where you can enter details of your return shipment as usual (return shipment feature will be eventually integrated into the new service in near future).