Allen Cell Discussion Forum

3D Visualization Workshop - Oct 1st 2019

For attendees of the 3D Visualization Workshop, which is a part of the BioImage Informatics 2019 conference held at the Allen Institute for Cell Science, if you have any questions during the workshop, we have helpers with Staff badge sprinkled throughout the conference room.

There is also a Slack channel dedicated for this event that we had sent out invites to the attendees.

And lastly, you can also post your questions here on the forum in the Software & Code category - other people might have the same questions and it’d help to address it early.

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  • Click on the [+ New Topic] button on the right side below the dark blue menu bar on the forum homepage and post away!
    ** Please don’t worry too much about what category, tag, etc. to use, as anything is editable even after posting, and we (admin) can also move posts to appropriate categories and such.

Please feel free to reach out anytime!

I attended this workshop (which was really fantastic!) and just wondering if the slides, links, comments etc that were on slack are they still available since the slack channel is no longer active?


@amycaitriona, Yes, we created the transcript from the Slack channel and emailed the participants from the workshop, so you should see that message! Thanks again for joining us at the Allen, and trying out the Segmenter. Let us know if there is anything else we may help with.

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That is great, thanks!!

Hi team,

I remember Susan talking at this event and mentioned your method for trying to essentially reconstruct the 100x Airyscan quality image with 20x Spinning Disk quality images.

I remember that your results improved significantly by adding an ‘autoalign’ step into the transition from your 20x to 100x images and that you had plans to look at direct vs daisy-chaining models, etc.

I was wondering if there had been any updates on these models and if your code for this was available on GitHub?

Thanks very much,


Hi Andrew,

Thanks for your interest. Releasing the first bioRxiv paper of our transfer function is currently on top of my list. I am trying to get it done in 1-1.5 months. Stay tuned:)

Thanks again,