Request for Spaceranger workflow update

[Helena Jun]

Dear Cumulus team,

Thank you for developing and sharing the cumulus workflows, which have been incredibly helpful for our research. I’m writing to kindly request an update of the spaceranger workflow to support the latest release (v.4.0.1).

The new version introduces key features like segmentation, and 10x genomics now strongly recommends using 4.0+ for future analyses. We and likely other users would greatly benefit from being able to run 4.0+ within the cumulus pipeline.  Please let me know if there is anything I can do to help test or support this update.

Thank you again for all your work!

[Yiming Yang]

Hello Helena,

Thanks for reaching! Supporting Space Ranger v4.0.1 is on our agenda. 

I have one question which may need your use case or experience: our current workflow wraps the "spaceranger count" command. For the segmentation feature, it requires using "spaceranger segment" command. So I wonder in your analysis, do you use both of them? And if so, how do you combine the results of 2 commands? Thanks!

Sincerely,

Yiming

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γνῶθι σεαυτόν.

[Helena Jun]

Hi Yiming,

Thank you for your reply!

Yes, we can use both of them in spaceranger v.4.0, which is one of the biggest strengths of this new version. We usually perform segmentation locally and separately after running the spaceranger count pipeline and if we want to use the original H&E for segmentation, we will align the cytassist image with the higher resolution H&E image via transformation prior to segmentation and nuclei labeling. 

Within spaceranger, I believe all these processes are included, which make our lives so much easier—aligning the cytassist image (--cytaimage) with the H&E image (--image) through their own image registration and some refinement processes, so that all these results can be shown on the same spatial coordinate space.

Please let me know if this answers your question. I’m happy to learn about this more and support your implementation!

Thank you,

Helena

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From: Yiming Yang <yang.y...@gmail.com>
Sent: Monday, July 21, 2025 7:57 PM
To: Helena Jun <junh...@broadinstitute.org>
Cc: Cumulus Support <cumulus...@googlegroups.com>
Subject: Re: Request for Spaceranger workflow update