SPHIRE

[Thorsten Wagner @pixelbaumarkt]

TomoTwin official release pt 1 🥳! After some code streamlining and writing documentation we’ve released the first stable build of TomoTwin. Here’s an example of TomoTwin picking Tc toxins based on a single reference without having to be trained on the protein beforehand. 🧵1/6

[Thorsten Wagner @pixelbaumarkt]

Finally, SPHIRE-crYOLO 1.8 is out and here is what is new:
1/4: It contains support for picking filaments and prominent particles in tomograms. Thanks to @TackeSebastian + @Zhexin_Wang for debugging this while tracing tomograms of the sarcomere!
#cryoem @mpimoph @SPHIRE_Package

[SPHIRE @SPHIRE_Package]

Huge kudos to @MStabrin, twitterless Luca Lusnig, @imagdoc , @taputechnic, twitterless Fabian Schoenfeld and @pixelbaumarkt for all the hard work :-)

[SPHIRE @SPHIRE_Package]

We are excited to announce the release of SPHIRE v1.4! Changes include: Improved helical support; GPU ISAC support; and AutoSPHIRE fully ready for TranSPHIRE to produce on-the-fly reconstructions during data acquisition!

https://t.co/N8xwuJCRpr

[Thorsten Wagner @pixelbaumarkt]

By picking ribosomes on 5 slices from 5 tomograms, crYOLO generalized well and picked ribosomes in new unseen tomograms.

[Thorsten Wagner @pixelbaumarkt]

We also applied it to viruses ( thanks @pnmshah ).

[Thorsten Wagner @pixelbaumarkt]

We are happy to invite brave people to test the beta version of crYOLO 1.8 which brings tomography support! Tutorial: https://t.co/GMBMcfdJz3

[SPHIRE @SPHIRE_Package]

We're happy to announce the release of TranSPHIRE! Use it to evaluate and optimize your data live at the microscope. Find the download + documentation + examples here: https://t.co/BL1ZR77W2L https://t.co/k0jUaH3RbX

[MPI Dortmund @mpimoph]

Looking for a software package for
fully-automated processing of #cryoEM datasets?
💾➡️💎

Check this

TranSphire: automated and feedback-optimized
on-the-fly processing for #CryoEM - by @Intein @maxplanckpress @gatsogia -published in @NatureComms

➡️https://t.co/JrQzzc3lGK

[SPHIRE @SPHIRE_Package]

GPU ISAC v2.3.2 is out! This hotfix release includes a major improvement in system memory usage, as well as several smaller quality of life improvements. Please find the download and release notes here: https://t.co/vHet5gQuWx

[SPHIRE @SPHIRE_Package]

GPU ISAC v2.3 it out! This milestone release provides a GPU-powered version of ISAC that runs on a single machine w/o the previous stack size limitations, and provides class averages in the known ISAC quality. Find the download link and documentation here: https://t.co/vHet5gQuWx

[Thorsten Wagner @pixelbaumarkt]

Cinderella 0.7 is out! New masking and with the help of @azazellochg I fixed several issues that occur in combination with Relion classes that lead to failed training. 2,300 Relion classes provided by @azazellochg were added to the general model. https://t.co/Rs0hgUFoMc

[SPHIRE @SPHIRE_Package]

The work was done by Fabian Schönfeld. Well done Fabian!

[SPHIRE @SPHIRE_Package]

We're happy to announce the release of GPU ISAC v2.2 (Beta)! Use it to quickly produce 2D class averages and screen your data. Find the download + documentation + examples here: https://t.co/vHet5gQuWx

[David Boyer @subletterdave]

Successfully got #cryolo to pick some pretty challenging amyloid fibril cryo-EM images about as good or better than a human! Should save weeks of time manually picking fibrils.

[Christos Gatsogiannis @gatsogia]

With heavy heart we had to postpone our #cryoEM symposium/workshop until next year.
Save the new dates:

23-27 April.2021, Heraklion Crete
Registration deadline: 30. Dec. 2020

More details here: https://t.co/TS4NJWobP5

[MPI Dortmund @mpimoph]

Two particle-picking procedures for filamentous
proteins: @SPHIRE_Package -crYOLO filament mode and
SPHIRE-STRIPER - @pixelbaumarkt et al. published by @Intein lab #cryoEM #DeepLearning in @ActaCrystD

https://t.co/ifu8JdXN5j

[SPHIRE @SPHIRE_Package]

@Ludo_cryoEM @thermosciEMSpec We show an example of the "on-the-fly-ness" for the machines we used for the experiments in supplementary figure 3 https://t.co/zHzooSRIAq. The curves will be shifted towards the lower right corner for stronger hardware.

[SPHIRE @SPHIRE_Package]

@Ludo_cryoEM @thermosciEMSpec If the data processing is able to keep up with the speed of the data collection highly depends on the specification of the machine it is running on and the strategy of the data acquisition. 100 micrographs per hour with 20 frames is much less demanding than 400mph with 100 frames

[SPHIRE @SPHIRE_Package]

@HaselbachLab @gatsogia @BolandLab_GE Unfortunately it is not ready for download, yet. But it will be available within the next weeks :)

[SPHIRE @SPHIRE_Package]

@MartinPacesa Thanks a lot! While crYOLO and Cinderella are already integrated, GPU ISAC is currently on the way and the feedback-driven optimization might be integrated in the future.

[SPHIRE @SPHIRE_Package]

TranSPHIRE - automated SPA processing on-the-fly during image recording. Includes a machine learning-based feedback loop that adapts the workflow to any given data set (incl. filaments) live during processing. Runs on a single workstation
https://t.co/jTEEPXVZ4Y