Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 8 Next »

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

  1. Navigate to ispyb.diamond.ac.uk

  2. Log in with your federal ID and password

  3. Click Proposals in the top left corner, and select the proposal and then the visit that you wish to register samples against

  4. Your selected proposal appears next to the Proposals button. Hover over your proposal, and select Phases from the dropdown menu which appears

  5. 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

  6. 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

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.

 More on individual sample upload...

  1. Log in following the instructions above, and click the + New Simple Sample button

  2. The acronym is automatically populated with that of the UAS sample you’re linking to. Make sure to change this to be unique

  3. Fill in the boxes with your sample information. Full descriptions of each field can be found below.

  4. You have the option here to select the data collection time in seconds. We recommend leaving this value at 600

  5. To correctly link samples to the capillary/container backgrounds that will be collected, you need to declare the capillary type:

    1. 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

    2. To reuse an existing background collection, select this from the list instead

    3. 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

  6. 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).

 more on multiple sample upload...

All samples in the csv file will be linked to the same UAS sample (with the associated risk assessment), so you may need multiple csv files to upload all your samples

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

  1. Log in following the instructions above, and click the + New Simple Sample button.

  2. 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.

  3. You have the option here to select the data collection time in seconds. We recommend leaving this value at 600.

  4. To correctly link samples to the capillary/container backgrounds that will be collected, you need to declare the capillary type:

    1. 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)

    2. To reuse an existing background collection, select this from the list instead

    3. 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

  5. Click Add sample.

  • No labels