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2022/02/08 - Microscope development meeting

Attendees

Attending:

  • Danail Stoychev
  • David Miguel Susano Pinto
  • Ian Dobbie
  • Julio Mateos-Langerak
  • Thomas Fish
  • Veronika Pfannenstill

Apologies:

Notes

  • fix on mosaic with deleting textures (cockpit #788)

    Cockpit #788 (PR) which closes Cockpit #787 has been merged but that reverts the Linux fix for cockpit #684 (part fix since that issue seems to actually be two issues). Need to check in Linux if issue returned.

    David will test it.

  • Microscope support for picam is broken (python-microscope/microscope#167)

    David says he thinks the picam is broken as it was rebased from a very old microscope version. Ian will test the pycam and fix if needed. See also meeting notes from 2021-10-12 meeting and notes on python-microscope/microscope#167

  • multi channel on one camera (cockpit#686)

    Danny is using the multi-channel on one camera, This ought to be merged.

  • digital z stack (cockpit#729, cockpit#691)

    Julio asks about digital Z stack and implementing similar behaviours for XY moves in a multi-position experiment. RedPitaya has wait states and some stages return a signal when reaching position but that would lead to non-uniform time interval.

  • slow multi-site experiment

    Julio has long lag between images in multi-site experiment, 10-12s between sites. Not sure why but believes that many operations here could be made async for speed.

  • truncated files

    If an experiment fails, user ends up with truncated dv files. The header is created ahead of time and then frames added to it. If experiment is not finished there will be missing frames and file will be smaller. Not all tools can handle it. If experiment is not finished not sure what is the best approach since we're left in an unkown state and may be better to stop messing with the file than potentially make things worse. A knowable user might be able to salvage some of the data.

    Decided not to be to clever about rewriting headers as we don't know where or how it failed.

  • duplicate events during snap with multiple cameras (cockpit#784)

    Julio has issue with duplicate events during snap. This crashes his executor with 2 cams and 2 lasers. This is not in the action table.

  • ImSwitch

    Someone is working on adding python-microscope support for ImSwitch. They have started with lasers and got Toptica iBeam and Cobolt lasers to work. This led to small fixes (see python-microscope/microscope#232, python-microscope/microscope#233, and python-microscope/microscope#234)

  • Hamamatsu (python-microscope/microscope#38)

    David getting the Hamamatsu camera control on Linux but only has one camera to test. Multiple cameras is tricky but no way to test. Julio might try the code on multiple cameras.

  • new microscope release

    David to make new release, mainly because currently we're incompatible with the last pyserial release (see python-microscope/microscope#233 and pyserial/pyserial#634).

    David will wait for Ian to check the picam code (we don't want to release if we're pretty sure it doesn't actually work).

  • Vortan VersaLase (python-microscope/microscope#230)

    Veronika working on VersaLase multi-laser engine. Mostly done and in final stages of debugging. Having problems with serial connection from computer to laser controller.

  • AO-tools

    Danny and Matthew have made a lot of changes on AO tools, both on the backend AO device but also on the UI.

  • Ian's old branches

    Ian to look at pycam on Microscope, and multi-channel single cam experiments, digital z stack for merging into the main branch of Cockpit.