measurePSF

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Lens paper data are single channel and they no longer have a clear purpose

1

The lens paper was being imaged to provide a quick proxy for assessing the overall microscope health. This was almost a subjective check: "If I can see lens paper at...

raacampbell

Test cleanup functions

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Commit bd21da6366f8f5a72d84aab0bd0944ea832c4b26 finally reapplies the scanner settings using a cleanup object, so they will be re-applied even if the acquisition fails and generates an error. We should test this at...

raacampbell

Save only lens paper and standard source channels for which there are connected PMTs

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The lens paper can produce a fairly large quantity of data (especially if run at multiple gains). So we don't want to be saving data for channels that don't have...

raacampbell

Look in the lens paper data from the current directory and extract the PMT gains from each file. Then acquire at the same gains with the standard source. This will...

raacampbell

PMT Gain is only for first PMT in lens paper and standard source

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In at least the lens paper and standard source examples, the gain value reported in the file name is for the first PMT only. If there is a mixture of...

raacampbell

Make a GitBook documentation site

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We should make a [gitbook](https://www.gitbook.com/) site explaining how to run everything here. The [Zapit docs are on Gitbook](https://zapit.gitbook.io/user-guide), for example. We have a lot of functions here and it will...

raacampbell

Rename this thing

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This repo is very definitely no longer "measurePSF". Alternatives: * multiphoton_standardisation * multiphoton_qc * scanimage_standardisation_tools * scanimage_qc_tools Once decided we need to rename a load of stuff because everything is...

raacampbell

Lens paper data are not acquired at any fixed gain

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We can, of course, determine gain from the TIFF header. However, I think somehow we need to ensure gain is consistent over recordings and time. This is not being done...

raacampbell