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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    ** 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wondering if the slides, links, comments etc that were on slack are they still available since the slack channel is no longer active?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,


I was wondering if I could get some help figuring out which package to use for visualizing cell images. I know that this process can be done using many different packages (skimage, pyplot, ipyvolume, etc). I was curious which packages your institute uses most frequently?

I only have a laptop at the moment so I find that a lot of visualizations take far too long to produce on Jupyter and often look blurred. Do you think that I should switch to a faster CPU? If so, what requirements would I need (in terms of memory, etc) to produce cleaner visualizations?

Also, really love the work you guys are doing and appreciate that you open source it! Thanks!

there are two packages I use a lot for visualizing cell images especially 3d images in juputer or in pure python: itkwidgets and napari.

hope you find them helpful :smile:

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