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  • 1.  10X Visium and Xenium sample preparation workflow advice

    Posted 08-20-2025 14:19

    Hi Everyone,

    I am posting this message on behalf  of Lesley Bechtold from the Jackson Labs:

    "We are currently preparing slides for our Single Cell Biology Group and our Mass Spectrometry group for both 10X Visium and xenium as well as mass spec imaging (MSI).  The samples are embedded in CMC (carboxymethyl cellulose), cryosectioned onto RNAse-free 10X slides (that have a serial number etched on them) for spatial'omics as well as Intellislides for MSI (metabolomics, proteomics and lipidomics).  The 10X slides have no identifying features on them except for the etched serial number.  We cannot add a label or any other identification to them.  The Intellislides for MSI have a barcode and we can't add anything to them either.  Keeping slides grouped together and delivered to the downstream services is painstaking. We have to manually copy the serial numbers and barcodes into our request system (we use iLabs).  We create a slide key and attach it to the iLabs request, which is shared amongst the groups.  We also create labels on the mailers, slide pouches, etc. but mistakes are still made.

     I'm wondering if any other histology groups are doing similar work and if they have found a system that works for them?"

    Please reply to this thread if you have any advice.

    Thanks!

    Jane

     

    Thank you.

     

    Lesley



    ------------------------------
    Jane Srivastava
    Flow Cytometry Core Director
    Gladstone Institute Flow Cytometry Facility
    San Francisco CA
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  • 2.  RE: 10X Visium and Xenium sample preparation workflow advice

    Posted 08-21-2025 09:05
    Hey Lesley and Jane,

    Interesting question. We do a small volume of the 10X slides for our fantastic Genomics group. When I reach the imaging portion of the workup, I scan the label/tissue and drop that image in a folder (labeled and dated w/ the researchers name). This works well for small volume work for slide ID.  For your MSI slides, I took a look at the slides online, is there anyway you could use those labels that many people use to label  the tops of cryo-tubes? Just cover up the logo on the slide, not the barcode? Or even a very tiny piece of lab tape? 


    Screenshot 2025-08-21 at 8.49.23 AM.png Screenshot 2025-08-21 at 9.01.50 AM.png

    Kathy





    Kathy Cormier
    Core Director and Science Accelerator
    Hope Babette Tang Histology Facility
    Koch Institute for Integrative Cancer Research at MIT
    500 Main Street, 76-182
    Cambridge, MA 02139
    617-258-8183
    cormier@mit.edu 
    RRID:SCR_019177
    https://ki.mit.edu/sbc/histology