Dear Lifei,

as far as I know, at the moment there is no software that does what you 
want. In Scipion we are actively working towards it and we are 
connecting the downstream processing of Scipion with the upstream 
driving of the microscope of SmartScope. We have succeeded to connect 
the information from particles, coordinates, micrographs, CTF, ... to 
the information of holes and squares, and we can successfully talk to 
Smartscope. The next step is to drive the acquisition towards the most 
needed/promising regions. If you want, we may have a separate 
conversation on this development and see how we could collaborate or 
help your problem once it is done.

Kind regards, Carlos Oscar

El 29/10/2023 a las 22:02, Lifei Fu escribió:
> Dear All,
> I am writing to inquire about tools that can efficiently sort micrographs by selected particles and visualize particle distribution within single-particle data processing software like Relion and Cryosparc. The objective is to correlate particle distribution with micrographs and squares for optimizing our data collection process and archiving strategies.
> For instance, after an overnight data collection session, we accumulated 2500 movies. Real-time data processing revealed that out of these, 60K good particles were used to reconstruct a 3.5 Å map following refinement and post-processing. However, during 2D classifications, it became evident that 80% of particles were side views, and increasing the number of top views could significantly enhance the map quality.
> The ideal approach focuses on obtaining more top views. Initially, we sorted micrographs based on the number of top views, identifying source micrographs and the top view distribution within the thin ice region, more like concentrating at the hole center. To optimize our data collection, we subsequently adjusted the off-center value to collect more top views.
> We can also integrate this approach with our serial EM naming conventions for movies, which follow this structure: Timestamp + protein name + grid number + grid type + square number + anchor points number + movie number. By sorting square numbers by top views particle number, we can correlate particle distribution (top views) with specific squares on the atlas map. This allows us to identify squares of similar quality for continued data collection, targeting micrographs that yield more top views.
> After checking data quality in real-time processing, we aim to track specific particle positions within the micrographs and correlate their distribution with specific squares. This feedback will be invaluable for optimizing our data collection process.
> After data processing, we wish to sort micrographs based on the number of 'good' particles. This will enable us to discard micrographs that do not contain beneficial particles, optimizing space on our workstation. Ideally, if we can set a threshold (e.g., 10 particles), the tool should automatically move micrographs with a particle count below this threshold into a designated folder, such as "bad micrographs."
> In practice, the particle orientation distribution and the ice thickness gradient variation are somewhat random or caused by the surface charging or buffer conditions. Most software can show coordinates on the micrographs after picking, but not for micrograph sorting by selected particles.
> If anyone is aware of a tool that aligns with these requirements or has insights into relevant features, your input would be greatly appreciated. Thank you in advance.
>
> Best regards
> Lifei
>
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