PDF summary generator for Live sessions

Hi CS users,

I’ve been working the last couple months on a python script that will generate a PDF report automatically from a CS Live session (related thread: Solutions for reporting from CryoSPARC Live session anyone? ). If the movies and metadata are still in their original locations, it will also generate some “bonus” plots that we’ve found helpful in analyzing which grid squares are yielding better CTF data or more particles. I’d be delighted if others gave it a try if you think it would be helpful for you / your users.

This explicitly doesn’t use cs tools, so that any past or present user can run it as part of an automated data transfer script or similar without having to go through the logins (maybe there’s an easy way around this, but regular python tools do a great job parsing).

I’m sure there are bugs hiding everywhere, especially for any workflow that doesn’t look like our standard ones, so reach out if you are running into issues. (CS folks – I hope this doesn’t infringe on copyright or anything; we’re hoping to use it to reduce documentation burden and increase some of the more analytical approaches to grid square choices. But if it does, reach out :slight_smile: ).

Script can be found here: GitHub - tlevitz/CryoSPARC_Live_Report: Generates a PDF report of a CryoSPARC Live session · GitHub

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Nice!! I love the physical location plots! I wonder if it would be possible to get atlas/square images from e.g. an appion database and overlay the metadata.. I’d love a version of this that works with leginon/appion although I realize that is probably a pretty small niche! :sweat_smile:

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I have something similar for EPU here, which at least eventually lets users compare side-by-side directly: GitHub - tlevitz/EPU_Generate_Report: A set of scripts that generates a pdf of a single particle EPU screening or collection session. · GitHub , so it may not be too heavy of a lift to modify it… My users are split whether they want one report for imaging and processing or two so they are separate for now. I haven’t used leginon/appion myself except in demos, but if you have a set directory structure I don’t think it would be too hard – feel free to connect via email and I’m happy to take a look :slight_smile:

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Both of these scripts seem super useful, thanks so much Talya!

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