We use a database called ISPyB as our laboratory information management system (LIMS). We encourage users to enter their sample information into ISPyB using a web interface before their visit, to reduce the amount of data entry which needs to take place during the experiment. Below are some step-by-step instructions for uploading your sample information.
What you will need
Your fed ID (in order to log in to the website)
An internet connected device
Your sample information
Validated samples in the experimental risk assessment on the UAS
When you create samples in ispyb, you will create a link to one of the samples you have previously entered into the UAS. This is so we can link ERA data to every sample brought to the beamline
There are two ways to upload your sample information: one at a time; or in bulk if you have your data in a suitable format.
Logging In
Navigate to ispyb.diamond.ac.uk
Log in with your federal ID and password
Click Proposals in the top left corner, and select the proposal and then the visit that you wish to register samples against
Your selected proposal appears next to the Proposals button. Hover over your proposal, and select Phases from the dropdown menu which appears
A table of the samples you created in the UAS will be displayed. Select the UAS sample to which you wish to link your sample/s
Click the “+ New Simple Sample” button
Only validated samples with acronyms will appear in this table, and samples can take up to three hours to be propagated from the UAS
A note on capillaries
Capillary choice will vary from experiment to experiment, more information on each capillary type can be found here. If you are unsure, please email your local contact.
When creating samples, you will be presented with a dropdown menu labelled “Capillary“. It will be pre-populated with templates for the various standard capillaries we use on I15-1.
Once you have created a sample, you will see a specific, named capillary in this list; in addition to the templates. The specific capillary will be selected by default the next time you return to the form: you should use this capillary for every subsequent sample which is to be mounted in the same type of capillary. You should only deselect this capillary should you want to add samples in a different type of capillary.
Uploading a Single Sample
If you’re only uploading one sample, you can upload your samples one at a time directly using the form on the website, which appears by default.
Log in following the instructions above, and click the + New Simple Sample button
The acronym is automatically populated with that of the UAS sample you’re linking to. Make sure to change this to be unique
Fill in the boxes with your sample information. Full descriptions of each field can be found below.
You have the option here to select the data collection time in seconds. We recommend leaving this value at 600
To correctly link samples to the capillary/container backgrounds that will be collected, you need to declare the capillary type:
To register that you intend to collect a new background collection for this (and potentially other) samples, select the relevant capillary type from the list (these will be a name only with no number)
To reuse an existing background collection, select this from the list instead (these will start with a number)
If your sample is to be collected without a container, or if you’d like to use a non-standard container, please speak to your local contact
Click Add sample.
We recommend reusing empty capillary data collections as much as possible! If all your samples will be packed into the same capillary type, then you should register one background data collection and reuse it for every other sample
Uploading Multiple Sample
You can upload multiple samples in one go by assembling your sample information into a csv file (i.e. a text file with the data columns separated by commas).
Step 1: Formatting the Data
The first step is to format the data correctly. Your csv file should have a header row as below, and then one sample per line. You can make a csv file directly from Excel by changing the file format in the “Save As…” dialogue, or you can download a template file.
Acronym,Composition,Density,Packing Fraction,Comments
Sample 23221,Fe3F3O(C6H3(CO2)2)3(H2O)12,1.232,0.55,As synthesised
Sample 23222,Fe3F3O(C6H3(CO2)2)3(H2O)12,1.204,0.51,Heated to 450 K and quenched
Sample 23223,Fe3F3O(C6H3(CO2)2)3(H2O)12,1.323,0.60,Heated to 450 K and slow cooled
Acronym is a string that describes the name of your sample, it should not contain any commas, and must be unique
Composition is the chemical composition of your sample. You may use parentheses, but not square brackets of curly braces. You should avoid using the “dot” convention for water of crystallisation
Density is the crystallographic density of your sample, i.e. how dense a single crystal or purely solid lump of your sample would be, in grams per cubic centimetre (g cm-3)
Packing Fraction is a measure of how densely packed your sample is into the capillary, relative to if it were a liquid and you poured it in. Most powders pack with a packing fraction of ~0.6, i.e. 60% of the capillary is sample and 40% is air. If you have a liquid, your packing fraction will likely be 1. If you have a very “fluffy” powder, it will likely be less that 0.6
Comments is an optional field where you can type a more verbose description of your sample. You may not include commas in your comment
Step 2: Upload the file
Log in following the instructions above, and click the + New Simple Sample button.
Select the file to be added using the Select File button. The contents of the file will be inspected, and any errors will be pointed out. If the file is good, File OK will appear.
You have the option here to select the data collection time in seconds. We recommend leaving this value at 600.
To correctly link samples to the capillary/container backgrounds that will be collected, you need to declare the capillary type:
To register that you intend to collect a new background collection for these (and potentially other) samples, select the relevant capillary type from the list (a new background will be created against the first sample in the file)
To reuse an existing background collection, select this from the list instead
If your sample is to be collected without a container, or if you’d like to use a non-standard container, please speak to your local contact
Click Add sample.
Irrespective of which of these methods you use to upload your sample information, you will have created a number of “Instances” - you can check these out by selecting Instances from the drop down menu.
Capillaries
Once you’ve created your sample instances, you local contact can extract from the database how many capillaries you will need and where to send them. You therefore must also follow these steps to associate a postal address with the session to enable the capillaries to be dispatched.
Step 1: Create a Lab Contact
If you have created the correct lab contact previously, you can skip this step and go straight to associating a contact with the session, see below.
From the dropdown menu, select “Lab Contacts”
Click the “Add Home Lab Contact” Button
Fill in everything up to the Dewar Return Details section, and click the add contact button when you are finished. The address that will be used on the shipping label will be as follows:
Contact Name Laboratory Name Street Address line 1 Street Address line 2 Street Address line 3 Laboratory City Laboratory Postcode Laboratory Country
Step 2: Associate Contact with Session
Now you’re created a lab contact, you need to associate that contact with the samples you just created.
Navigate to the “Shipments” section under the dropdown menu
You should see a shipment called cy12345-0_Shipment1 where cy12345 is your proposal code. Click this shipment to edit the details
Click to edit the Outgoing Lab Contact, and select the relevant lab contact to whom the capillaries should be posted. If there are no contacts in this list, you will need to create one following the instructions above.
