Elphys/General experiment gui

[roskalab]

• scalable: generic, elphys, rc microscope gui, multichannel mea
• animal parameters
• exp data display/eval status
• select stim/start exp
• anesthesia log
• filterwheels
• network connectivity status
• record sync signals
• data converters: mat, tiff

Minor details:

• file name generation takes place here, then this is distributed to other applications
• each application generates its file locally, gui puts them together
• bullseye, set background color
• pixel size calibration, intensity calibration (matching intensities of different setups)

[roskalab]

=== Stimulation possibilities === -LED -2p - pockel cell control -projector -Screen for in vivo experiments, flieckering control (duty cycle and timing needs to be calculated, 128x128 um@2 pixel/um, 40x40 um@ 6 pixel 8 Hz frame rate, flyback time should not be less than 30%)

=== Data acquisition channels ===

• ca imaging
• traditional electrode recording
• extra cellular electrode recording - multiple channels

=== Experiment control ===

• select stimulation output: projector, screen, led, 2p, uled
• select data acquisition channels
• any combination shall be supported
• experiment parameters:
  • list parameters, play preview of stimulation (accelerate, play, stop)
  • tabs for led and 2p (duration, intensity, flash duration, visualize timing)
• loop across depth and laser intensity

=== GUI ===

• live display of electrophys, ca (user selected box, difference between two user selected boxes)
• try to eliminate imaging gui - only live 2p image shall be left on that GUI
• highlight tab if corresponding stim/acquistion channel selected
• z stack: depth and intensity adjustment
• zoom into plot, show value at cursor

=== Experiment data ===

• hdf5/mat
• tiff: sequence/separate files in a folder, include sync data -txt: time, elphys, sync

=== Data display app - traceviewer2 ===

• align ca data with stim video/tiff generator
• plot under ca frame, show position, sync data
• list files, plots from user selected

[roskalab]

Scanner timing: scan size [um] resolution [pixel/um] line frequency [Hz] line time [us] off time [us] duty cycle [%] frame rate [Hz] 25 2.0 2367.0 423.0 298.0 70.0 45.0 25 4.0 1826.0 548.0 298.0 54.0 17.9 25 6.0 1487.0 673.0 298.0 44.0 9.8 40 2.0 2010.0 498.0 298.0 60.0 24.4 40 4.0 1434.0 698.0 298.0 43.0 8.8 40 6.0 1114.0 898.0 298.0 33.0 4.6 128 2.0 1067.0 938.0 298.0 32.0 4.1 128 4.0 634.0 1578.0 298.0 19.0 1.2

Constraints:

• 200 Hz line scan frequency, min 30 % duty cycle

[roskalab]

Idea 1: Ca Imaging software shall not use qt gui. Only live image is to be displayed on a single pygame graphics window.

Idea 2: Why don't we merge imaging and elphys/control computers? Elphys and two photon data acquisition would still take place on separate daq boards. Ca imaging might eat up the windows process's memory space. Coexistence with legacy but working setups is difficult because of daq swapping and rewiring.

Challenge: Better RAM utilization. Perhaps using OpenSUSE? Infrared camera driver might be an issue and getting it work might take long including learining the OS itself. The problem needs to be addressed on a windows system, perhaps a win 7 64 bit/python 64 bit is the way to go.

Idea3: Instead of Gui poller thread, separate process shall be used as a poller. Qt signals cannot be used between processes. Socket or queue can be an option. Data can be exchanged between processes by queues. The biggest amount of data to be sent from data acquisition to GUI is a ca image and ca/elphys traces.

[roskalab]

GUI shall be able to handle landmarks