Structure revamp and new fw capabilities updates

[ChucklesOnGitHub]

Fixes #45
Fixes #58
Fixes #55
Fixes #52
Fixes #48
Fixes #40
Fixes #26

[ChucklesOnGitHub]

Edit reference to v3.4 as it will be 4.0. It won't. However, .4 will be removed from the device name in the device manager. Revise screenshots once fw includes this change. Upload new uploader @aacuevas

[ChucklesOnGitHub]

Check for channel name changes before uploading. Also, even though Aux Input can be used for LED on/off, it may be better to specify that Input triggers is tied to the LEDRespectsTrigger property while Aux Input is not.

[cjsha]

do we need a banner informing people that the most recent version of the software supports the most recent version of the daq firmware?

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beyond the scope of this PR, but we need to go through and clear up the formatting to make these docs easier to read. For example:

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I think the tutorials need to be updated for the new version of the library?

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I almost feel like the User Guide can fall under FAQ. For example, there can be a few questions "How do I plan ahead for miniscope surgery?" "Are there resources to learn how to do surgery?" "How do I habituate animals?" etc. If you agree, the User Guide can just be subsumed by the FAQ. I just think that there are too many guides between the software guide in the hardware guide and the user guide on the front page

[ChucklesOnGitHub]

Corraling outstanding ToDos:

• Upload updater once finalized version is available.
• Update screenshots with latest fw: device manager listing, fw dropdown and software channels could change. Check no workflow images are cropped.
• Update references to names in device manager or channels, if required
• Add site-wide banner informing people that the most recent version of the software supports the most recent version of the daq firmware
• linkchecks: exlude chroma? it always times out
• wait for software to be published to push
• check videos and worfklow copy/download work in the remote build

Addressing some other comments:

• I checked that the tutorials worked in the new version of the library. What did you see needed updating, Cris?
• The reason I call it a User Guide and not a FAQ is that content in a guide have specific places to be, each section has titles grouping topics together, instead of being a catch-all. We already have User Guides in our other docs to this effect. Adding a FAQ could be useful but it really has to be frequent questions. Ultimately, the answers to the FAQs should be links to the existing docs addressing these. Idk maybe I'm being square. Anyways, out of scope for this PR.

[ChucklesOnGitHub]

In my local build some of the workflow images are cropped, would you know @cjsha why this could be? e.g. Software-Guide/trigger

[cjsha]

I checked that the tutorials worked in the new version of the library. What did you see needed updating, Cris?

Sorry I think you're right. I think the part that might require updating is about syncing data. We should mention the FrameNumber member of the UclaMiniscopeV4Frame that Aaron recently added. Essentially, every frame captured by the DAQ corresponds to a TTL pulse and increments the FrameNumber by one. However, it could be the case that the frame drops between the DAQ and the PC which means that you could get a TTL toggle on Sync Out but no image corresponding to this TTL pulse. In this case, you can count the number of TTL rising/falling edges and use FrameNumber to know which TTL pulse corresponds to which frame.

[cjsha]

I think my qualm with the user guide is that the software guide feels like the real user guide and the user guide feels more like "extra information".

[cjsha]

In my local build some of the workflow images are cropped, would you know @cjsha why this could be?

not sure how this happened but it's because the images themselves are cropped.

[cjsha]

I submitted my feedback and made some changes to the docs in their current state. I understand that more changes are to come before this is fully merged, but I feel comfortable for you to take care of that stuff without another round of review if you feel that way too. so I will approve this PR already. with that said, lmk if you want me to look at anything

[cjsha]

additional changes that need to be made:

• update workflows to match the new frame member names. make sure this is reflected in the content as well
• aux is Din1, trigger is Din0

[cjsha]

Remaining items:

• wait for software to be published to push
• check videos and worfklow copy/download work in the remote build