I would also like to be able to switch between the two-parameter graph view, and a histogram view - sometimes it is useful to be able to view a histogram of e.g. defocus or astigmatism, to get a sense of the distribution of the data.
Cheers
Oli
I’d also like to be able to curate based on the local defocus variation - I think a non-physical defocus variation is an easy parameter to use for rejection. Likewise, sorting by relative ice thickness would also be useful.
Cheers
Oli
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One more thought - the exposure curation tool, apart from being useful for curating exposures, is also useful as just a viewer, for exploring the dataset. Unfortunately, once you click done, you can no longer use it for that purpose. Would it be possible to alter it such that after submission the user can no longer submit, but can still interact with the dataset and view micrographs? The individual view with the CTF and morion correction info, as well as the micrograph, is particularly useful.
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Text entry boxes work if you type the number, then click outside the box, then hit tab. Bug.
I agree a simpler way to cull the data would be useful. For instance, extreme outliers ruin the scale of the axes and thus the usefulness of the tool. I typically have to curate first to remove extreme outliers of all parameters, create the outputs, and relaunch the tool on the already curated dataset.
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Yes I have also encountered this - e.g. displaying the CTF cross correlation data is usually useless because one outlier will throw it off. I wonder if one way to go would be to rescale the axes after accepting a selection - that should alleviate the outliers issue a bit.
Hi Suhail - one more suggestion in the rework of this tool - could you please write out the thresholds that were used to the log file? This is useful for record keeping and writing methods later - e.g. “all micrographs with CTF fit worse than x Å or defocus greater than y µm were rejected” etc
Inspect picks. writes out the thresholds used, but exposure curation currently does not.
Cheers
Oli
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I like the idea of curating exposures, including by average intensity. Wouldn’t it be trivial to parallelize
with cpus to speed up the average value part? It does warn that it takes a long time, but for a large data set it is really long time.
Thanks for all your efforts! George
When using larger datasets (e.g. 13000 mics) the curate micrographs tool is entirely unusable - any prospects for speeding it up in the overhaul? Is there a timeline for the new version?
Hi @sdawood - is there any timeline for the overhaul of Curate Micrographs? It is becoming increasingly unusable as typical dataset sizes have increased with wider availability of K3 detectors - e.g with 15k micrographs it is really not practical. Even just addition of non-interactive thresholds (as exist now for Inspect Particles) would make a big difference! Hopefully in the next version?
Hi everyone,
Now that v3 and the newly redesigned Live application have been released, we are focused on updating all interactive jobs. This includes the significant changes to exposure curation that has been in the works for some time now. Please keep an eye out for updates in the next few weeks!
- Suhail
Hi Suhail,
I’m wondering if I can have the list of all accepted images’ names in the Curate Exposure Job? As I’m going to subtract gold beads from my micrographs by using IMOD software automatically, before that, if I can first trash all the un-accepted images in the Curate Exposure Job, it might be more efficient for the later steps.
Best,
Chuchu
Hi,
It would be nice to have a quick way to see the selection/rejection criteria (like selected images or thresholds for selected images) that were used in a previous job of Exposure Curation e.g. in the input/output mask.
Best,
christian
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@sdawood, using version 3.2 of Cryosparc and currently frustrated by a number of bugs with manual curation. Sliders update slowly and inputting a value seems to sometimes apply that value to another parameter (ie. changing ice thickness seems to apply changes to eg. total motion). Is the overhaul of this feature still in train?
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It would be nice to see the cutoffs that were applied in the curate exposure log after the job has been completed, sometimes I don’t keep track and don’t remember what cutoffs I actually applied
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In addition, can we have inputs in the job to specify the cutoffs automatically? I usually use similar values anyways, so often there is no reason for me to actually look at the micrographs.
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Hi @sdawood - is this still in the works? Even a small, temporary update would be appreciated, e.g. adding non-interactive thresholds like for inspect picks & outputting threshold values to the log, if the more substantial rework will still take some time?
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It would be great if exposure curation generated a summary of statistics in the log file (or maybe as a pdf attached to the log file. E.g. a histogram of each parameter (or at least defocus, relative ice thickness and CTF fit res), with mean, min and max values. This would be useful for record keeping and adjusting downstream processing (e.g. the average defocus is useful to know in guiding what box size to use).
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Thanks @olibclarke,
Thank you for the suggestions! We’ll make sure to output these statistics in the event log so that they’re available for the reasons you mentioned above.
- Suhail
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how about “automatically curate exposures”? with job builder values for cutoffs? and/or “use values from similar job”. basically, I developed whole workflow on subset of mics, now want to repeat on whole dataset, have to wait for CTF to finish before the auto queue of the whole processing pipeline. obv same applies for inspection of particle picks. THANKS!
Hi @CryoEM1 ,
Thanks for the suggestion. Indeed, it would be great to circumvent the interactive process and automatically apply thresholds to exposures based on a set of parameters at build time. This is on our roadmap - I’ll reply to this topic when we have an update!
- Suhail