├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── control ├── fluidics │ └── common_fluidics_programs │ │ └── ROUND1_ONLY.csv └── run_opm_iterative_stagescan_GUI.py ├── napari-control ├── opm_iterative_control.py ├── opm_timelapse_control.py ├── opm_timelapse_reconstruction.py ├── src │ ├── OPMIterative.py │ ├── OPMMirrorReconstruction.py │ ├── OPMMirrorScan.py │ ├── OPMStageMonitor.py │ ├── OPMStageScan.py │ ├── OPM_main.py │ ├── hardware │ │ ├── APump.py │ │ ├── ASI.py │ │ ├── AbstractValve.py │ │ ├── HamiltonMVP.py │ │ ├── OPMNIDAQ.py │ │ └── PicardShutter.py │ └── utils │ │ ├── autofocus_remote_unit.py │ │ ├── data_io.py │ │ ├── flat_field.py │ │ ├── fluidics_control.py │ │ ├── image_post_processing.py │ │ └── opm_psf.py └── test.gif ├── napari_opm_pymmcoreplus.py ├── pycromanager-control ├── data_io.py ├── run_opm_galvoscan.py └── run_opm_stagescan.py └── reconstruction ├── data_io.py ├── flat_field.py ├── image_post_processing.py ├── localize_gui.py ├── localize_skewed.py ├── opm_psf_520_nm.tif ├── opm_psf_580_nm.tif ├── opm_psf_670_nm.tif ├── recon_opm_galvoscan.py ├── recon_opm_stagescan.py ├── run_opm_galvoscan.py └── run_opm_stagescan.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/.gitmodules -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/README.md -------------------------------------------------------------------------------- /control/fluidics/common_fluidics_programs/ROUND1_ONLY.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/control/fluidics/common_fluidics_programs/ROUND1_ONLY.csv -------------------------------------------------------------------------------- /control/run_opm_iterative_stagescan_GUI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/control/run_opm_iterative_stagescan_GUI.py -------------------------------------------------------------------------------- /napari-control/opm_iterative_control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/opm_iterative_control.py -------------------------------------------------------------------------------- /napari-control/opm_timelapse_control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/opm_timelapse_control.py -------------------------------------------------------------------------------- /napari-control/opm_timelapse_reconstruction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/opm_timelapse_reconstruction.py -------------------------------------------------------------------------------- /napari-control/src/OPMIterative.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPMIterative.py -------------------------------------------------------------------------------- /napari-control/src/OPMMirrorReconstruction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPMMirrorReconstruction.py -------------------------------------------------------------------------------- /napari-control/src/OPMMirrorScan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPMMirrorScan.py -------------------------------------------------------------------------------- /napari-control/src/OPMStageMonitor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPMStageMonitor.py -------------------------------------------------------------------------------- /napari-control/src/OPMStageScan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPMStageScan.py -------------------------------------------------------------------------------- /napari-control/src/OPM_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/OPM_main.py -------------------------------------------------------------------------------- /napari-control/src/hardware/APump.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/APump.py -------------------------------------------------------------------------------- /napari-control/src/hardware/ASI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/ASI.py -------------------------------------------------------------------------------- /napari-control/src/hardware/AbstractValve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/AbstractValve.py -------------------------------------------------------------------------------- /napari-control/src/hardware/HamiltonMVP.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/HamiltonMVP.py -------------------------------------------------------------------------------- /napari-control/src/hardware/OPMNIDAQ.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/OPMNIDAQ.py -------------------------------------------------------------------------------- /napari-control/src/hardware/PicardShutter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/hardware/PicardShutter.py -------------------------------------------------------------------------------- /napari-control/src/utils/autofocus_remote_unit.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/autofocus_remote_unit.py -------------------------------------------------------------------------------- /napari-control/src/utils/data_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/data_io.py -------------------------------------------------------------------------------- /napari-control/src/utils/flat_field.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/flat_field.py -------------------------------------------------------------------------------- /napari-control/src/utils/fluidics_control.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/fluidics_control.py -------------------------------------------------------------------------------- /napari-control/src/utils/image_post_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/image_post_processing.py -------------------------------------------------------------------------------- /napari-control/src/utils/opm_psf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari-control/src/utils/opm_psf.py -------------------------------------------------------------------------------- /napari-control/test.gif: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /napari_opm_pymmcoreplus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/napari_opm_pymmcoreplus.py -------------------------------------------------------------------------------- /pycromanager-control/data_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/pycromanager-control/data_io.py -------------------------------------------------------------------------------- /pycromanager-control/run_opm_galvoscan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/pycromanager-control/run_opm_galvoscan.py -------------------------------------------------------------------------------- /pycromanager-control/run_opm_stagescan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/pycromanager-control/run_opm_stagescan.py -------------------------------------------------------------------------------- /reconstruction/data_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/data_io.py -------------------------------------------------------------------------------- /reconstruction/flat_field.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/flat_field.py -------------------------------------------------------------------------------- /reconstruction/image_post_processing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/image_post_processing.py -------------------------------------------------------------------------------- /reconstruction/localize_gui.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/localize_gui.py -------------------------------------------------------------------------------- /reconstruction/localize_skewed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/localize_skewed.py -------------------------------------------------------------------------------- /reconstruction/opm_psf_520_nm.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/opm_psf_520_nm.tif -------------------------------------------------------------------------------- /reconstruction/opm_psf_580_nm.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/opm_psf_580_nm.tif -------------------------------------------------------------------------------- /reconstruction/opm_psf_670_nm.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/opm_psf_670_nm.tif -------------------------------------------------------------------------------- /reconstruction/recon_opm_galvoscan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/recon_opm_galvoscan.py -------------------------------------------------------------------------------- /reconstruction/recon_opm_stagescan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/recon_opm_stagescan.py -------------------------------------------------------------------------------- /reconstruction/run_opm_galvoscan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/run_opm_galvoscan.py -------------------------------------------------------------------------------- /reconstruction/run_opm_stagescan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QI2lab/OPM/HEAD/reconstruction/run_opm_stagescan.py --------------------------------------------------------------------------------