SRS mail-in

This page contains information for beamline scientists running mail-in samples at 11-ID-B and 17-BM.

Preparing and Shipping Kits to Users

1. Once a user has submitted a sample base request AND confirmed it, add 1 or 2 barcodes (ANL20PDFXXXXX or ANL20XRDXXXXX) with 20 samples each to their proposal in the staff portal. Unique barcodes must be assigned to each new cartridge. All replacement cartridges (i.e. lost in mail, broken, contaminated) must be assigned a new barcode.
2. Assemble a mail-in kit and package in small box. Use the PI's address from the proposal system unless otherwise notified by the user. The user is responsible for notifying you promptly of any changes to their address. The kit components are as follows:
   1. mail-in cartridges + lids (1 or 2/proposal): custom printed by AES [include link to drawing, only for internal use] and labelled with QR code + human readable label
   2. kapton capillaries (20/cartridge): 0.0395" ID, 0.0435" OD and 17.5mm length, available pre-cut from Microlumen (P/N Code 395-II PI x 17.5mm, 5000 Pcs min = $0.30/each, Lead-time is 3-4 weeks) or in 12" lengths from Cole-Parmer (Item # EW-95820-09; Masterflex Transfer Tubing, Polyimide, 0.0395" ID x 0.0435" OD, 12"L; 5/PK).
   3. rubber bands (4/cartridge): small poly bands, available from any pharmacy or beauty supply store
   4. bubble wrap
   5. printed instructions (online version available here)
   6. address label with beamline info
3. For domestic shipments, the mailer containing the kit can be left in the outbox or on the table in 433. For international shipments, an ANL-126C must be submitted in XINK. Attach the shipping order to the package and drop off at the T-run in the APS stockroom. ANL-126C-55776 has the correct information for the 11-ID-B mail-in kit.
4. Email users to confirm the mail-in kits have been shipped but are not trackable. Include an electronic copy of the mail-in kit instructions.

Running mail-in samples

1. Load cartridges into "Lego"-style mount with the side labelled "Front"/"APS Mailin" facing downstream (11-ID-B).
2. at the command prompt: clear old macro files and pickles by running:

   python new_exp.py 

3. Create file 'barcode.out' in the ~/macros/MailinScripts directory. List the positions and barcodes of each sample holder. Use 'barcode_manual.out' as a model.
4. at the command prompt: to retrieve sample information from the database, run:

   python barcodeRetrieve.py 

5. at the command prompt: to create a prescreening macro for all the samples, run:

   python prescreenmaker.py 

6. in specfe: change directories to ~/macros/MailinScripts and compile the prescreen macro:

   qdo ./prescreenmaker.mac 

7. in specfe: run the prescreen macro to determine the optimal exposure times for each sample:

   prescreen_mailin() 

8. at the command prompt: after prescreening is finished, create a data acquisition macro for all samples:

   python scanmaker.py 

9. in specfe: compile the prescreen macro:

   qdo ./scanmaker.mac 

10. in specfe: run the data acquisition macro to collect data for all samples:

    run_mailin() 

Uploading Data from the data management system to Globus

Once the data has been collected, the following steps are required to upload the data to Globus:

1. allow up to 24 hours for data to be copied from sector 11 machines to servers accessible by Data Management system
2. add the mail-in proposals to the schedule for the current run (if from previous runs, this will not be possible)
3. ssh into the Data Management Machine for your beamline
4. load DM scripts
5. upload data (tiffs) from <mailinbarcodenumber> to GUP-<mailinproposalnumber>. Use the --proposal-id=<mailinproposalnumber> modifier to automatically include all users from the proposal OR manually add users after initiating the upload (if proposal from previous run)
6. email the users after the data is uploaded with instructions on accessing their data

Details on the credentials and commands for the Data Management Machine are available here.

Frequently Asked Questions

A list of frequently asked questions/complaints/etc. is here.