.pre-commit-config.yaml
LICENCE
MANIFEST.in
THANKS.md
pyproject.toml
readme.md
requirements.txt
docs/CODE_OF_CONDUCT.md
docs/CONTRIBUTING.md
docs/banner.png
docs/config.md
docs/formats.md
docs/gonio.md
docs/gui.md
docs/index.md
docs/make_programs_md.py
docs/merlin.md
docs/network.md
docs/programs.md
docs/setup.md
docs/tem_api.md
docs/tvips.md
scripts/__init__.py
scripts/browser.py
scripts/center_images_smv.py
scripts/diagnose_beam_drift.py
scripts/learn.py
scripts/make_interval_movie.py
scripts/make_serialed_movie.py
scripts/process_dm.py
scripts/process_tpx.py
scripts/process_tvips.py
scripts/viewer.py
src/instamatic/__init__.py
src/instamatic/_collections.py
src/instamatic/_typing.py
src/instamatic/acquire_at_items.py
src/instamatic/admin.py
src/instamatic/banner.py
src/instamatic/browser.py
src/instamatic/controller.py
src/instamatic/exceptions.py
src/instamatic/goniotool.py
src/instamatic/gridmontage.py
src/instamatic/image_utils.py
src/instamatic/imreg.py
src/instamatic/io.py
src/instamatic/main.py
src/instamatic/montage.py
src/instamatic/tools.py
src/instamatic.egg-info/PKG-INFO
src/instamatic.egg-info/SOURCES.txt
src/instamatic.egg-info/dependency_links.txt
src/instamatic.egg-info/entry_points.txt
src/instamatic.egg-info/requires.txt
src/instamatic.egg-info/top_level.txt
src/instamatic/TEMController/TEMController.py
src/instamatic/TEMController/__init__.py
src/instamatic/TEMController/microscope.py
src/instamatic/TEMController/microscope_client.py
src/instamatic/calibrate/__init__.py
src/instamatic/calibrate/calibrate_beamshift.py
src/instamatic/calibrate/calibrate_brightness.py
src/instamatic/calibrate/calibrate_directbeam.py
src/instamatic/calibrate/calibrate_imageshift12.py
src/instamatic/calibrate/calibrate_movie_delays.py
src/instamatic/calibrate/calibrate_stage_lowmag.py
src/instamatic/calibrate/calibrate_stage_mag1.py
src/instamatic/calibrate/calibrate_stage_motion.py
src/instamatic/calibrate/calibrate_stage_rotation.py
src/instamatic/calibrate/calibrate_stage_translation.py
src/instamatic/calibrate/calibrate_stagematrix.py
src/instamatic/calibrate/center_z.py
src/instamatic/calibrate/filenames.py
src/instamatic/calibrate/fit.py
src/instamatic/camera/CCDCOM.h
src/instamatic/camera/CCDCOM2_x64_gatan.dll
src/instamatic/camera/CCDCOM2_x64_simulation.dll
src/instamatic/camera/CCDCOM2_x86_gatan.dll
src/instamatic/camera/CCDCOM2_x86_simulation.dll
src/instamatic/camera/EMCameraObj.dll
src/instamatic/camera/__init__.py
src/instamatic/camera/camera.py
src/instamatic/camera/camera_base.py
src/instamatic/camera/camera_client.py
src/instamatic/camera/camera_emmenu.py
src/instamatic/camera/camera_gatan.py
src/instamatic/camera/camera_gatan2.py
src/instamatic/camera/camera_merlin.py
src/instamatic/camera/camera_serval.py
src/instamatic/camera/camera_simu.py
src/instamatic/camera/camera_timepix.py
src/instamatic/camera/gatansocket3.md
src/instamatic/camera/gatansocket3.py
src/instamatic/camera/merlin_io.py
src/instamatic/camera/mpxhwrelaxd.dll
src/instamatic/camera/timepix.lockfile
src/instamatic/camera/videostream.py
src/instamatic/camera/tpx/171207_with_flatfield.bpc
src/instamatic/camera/tpx/171207_with_flatfield.bpc.dacs
src/instamatic/camera/tpx/HW.dacs
src/instamatic/camera/tpx/config.txt
src/instamatic/config/__init__.py
src/instamatic/config/autoconfig.py
src/instamatic/config/config_updater.py
src/instamatic/config/defaults.yaml
src/instamatic/config/settings.yaml
src/instamatic/config/utils.py
src/instamatic/config/alignments/neutral.yaml
src/instamatic/config/calibration/orius.yaml
src/instamatic/config/calibration/simulate.yaml
src/instamatic/config/calibration/timepix.yaml
src/instamatic/config/calibration/tvips-f416.yaml
src/instamatic/config/camera/merlin.yaml
src/instamatic/config/camera/orius.yaml
src/instamatic/config/camera/serval.yaml
src/instamatic/config/camera/simulate.yaml
src/instamatic/config/camera/simulateDLL.yaml
src/instamatic/config/camera/timepix.yaml
src/instamatic/config/camera/tvips-f416.yaml
src/instamatic/config/camera/tvips-xf416.yaml
src/instamatic/config/microscope/fei_simu.yaml
src/instamatic/config/microscope/fei_themisZ.yaml
src/instamatic/config/microscope/jeol-1400.yaml
src/instamatic/config/microscope/jeol.yaml
src/instamatic/config/microscope/simulate.yaml
src/instamatic/config/scripts/close_down.py
src/instamatic/config/scripts/focus_mode.py
src/instamatic/config/scripts/hello_world.py
src/instamatic/config/scripts/readme.md
src/instamatic/config/scripts/search_mode.py
src/instamatic/config/scripts/showcase_movie.py
src/instamatic/experiments/__init__.py
src/instamatic/experiments/experiment_base.py
src/instamatic/experiments/autocred/__init__.py
src/instamatic/experiments/autocred/experiment.py
src/instamatic/experiments/cred/__init__.py
src/instamatic/experiments/cred/experiment.py
src/instamatic/experiments/cred_gatan/__init__.py
src/instamatic/experiments/cred_gatan/experiment.py
src/instamatic/experiments/cred_tvips/__init__.py
src/instamatic/experiments/cred_tvips/experiment.py
src/instamatic/experiments/fast_adt/__init__.py
src/instamatic/experiments/fast_adt/experiment.py
src/instamatic/experiments/red/__init__.py
src/instamatic/experiments/red/experiment.py
src/instamatic/experiments/serialed/__init__.py
src/instamatic/experiments/serialed/experiment.py
src/instamatic/formats/__init__.py
src/instamatic/formats/adscimage.py
src/instamatic/formats/csvIO.py
src/instamatic/formats/mrc.py
src/instamatic/formats/util.py
src/instamatic/formats/xdscbf.py
src/instamatic/gui/__init__.py
src/instamatic/gui/about_frame.py
src/instamatic/gui/autocred_frame.py
src/instamatic/gui/base_module.py
src/instamatic/gui/click_dispatcher.py
src/instamatic/gui/console_frame.py
src/instamatic/gui/cred_fei_frame.py
src/instamatic/gui/cred_frame.py
src/instamatic/gui/cred_tvips_frame.py
src/instamatic/gui/ctrl_frame.py
src/instamatic/gui/debug_frame.py
src/instamatic/gui/defocus_button.py
src/instamatic/gui/fast_adt_frame.py
src/instamatic/gui/gui.py
src/instamatic/gui/io_frame.py
src/instamatic/gui/jobs.py
src/instamatic/gui/machine_learning_frame.py
src/instamatic/gui/modules.py
src/instamatic/gui/mpl_frame.py
src/instamatic/gui/red_frame.py
src/instamatic/gui/sed_frame.py
src/instamatic/gui/videostream_frame.py
src/instamatic/gui/videostream_processor.py
src/instamatic/microscope/__init__.py
src/instamatic/microscope/base.py
src/instamatic/microscope/client.py
src/instamatic/microscope/microscope.py
src/instamatic/microscope/utils.py
src/instamatic/microscope/components/__init__.py
src/instamatic/microscope/components/deflectors.py
src/instamatic/microscope/components/lenses.py
src/instamatic/microscope/components/stage.py
src/instamatic/microscope/components/states.py
src/instamatic/microscope/interface/__init__.py
src/instamatic/microscope/interface/fei_microscope.py
src/instamatic/microscope/interface/fei_simu_microscope.py
src/instamatic/microscope/interface/jeol_microscope.py
src/instamatic/microscope/interface/simu_microscope.py
src/instamatic/neural_network/__init__.py
src/instamatic/neural_network/neural_network.py
src/instamatic/neural_network/preprocess.py
src/instamatic/neural_network/preprocess_SerialRED.py
src/instamatic/neural_network/weights-py2.p
src/instamatic/neural_network/weights-py3.p
src/instamatic/processing/ImgConversion.py
src/instamatic/processing/ImgConversionDM.py
src/instamatic/processing/ImgConversionTPX.py
src/instamatic/processing/ImgConversionTVIPS.py
src/instamatic/processing/PETS_input_factory.py
src/instamatic/processing/PETS_input_keywords.csv
src/instamatic/processing/XDS_template.inp
src/instamatic/processing/XDS_template.py
src/instamatic/processing/__init__.py
src/instamatic/processing/find_crystals.py
src/instamatic/processing/find_crystals_ilastik.py
src/instamatic/processing/find_holes.py
src/instamatic/processing/flatfield.py
src/instamatic/processing/stretch_correction.py
src/instamatic/server/TEMServer_FEI.py
src/instamatic/server/__init__.py
src/instamatic/server/cam_client.py
src/instamatic/server/cam_server.py
src/instamatic/server/dials_server.py
src/instamatic/server/goniotool_server.py
src/instamatic/server/serializer.py
src/instamatic/server/tem_client.py
src/instamatic/server/tem_server.py
src/instamatic/server/vm_ubuntu_server.py
src/instamatic/server/xds_server.py
src/instamatic/simulation/__init__.py
src/instamatic/simulation/camera.py
src/instamatic/simulation/crystal.py
src/instamatic/simulation/grid.py
src/instamatic/simulation/sample.py
src/instamatic/simulation/stage.py
src/instamatic/simulation/warnings.py
src/instamatic/utils/__init__.py
src/instamatic/utils/beamstop.py
src/instamatic/utils/deprecated.py
src/instamatic/utils/domains.py
src/instamatic/utils/high_precision_timers.py
src/instamatic/utils/iterating.py
src/instamatic/utils/native.py
src/instamatic/utils/progress.py
src/instamatic/utils/singleton.py
src/instamatic/utils/spinbox.py
src/instamatic/utils/xds_parser.py
src/instamatic/utils/yaml.py
tests/__init__.py
tests/conftest.py
tests/test_camera.py
tests/test_collections.py
tests/test_ctrl.py
tests/test_deprecated.py
tests/test_experiments.py
tests/test_formats.py
tests/test_grid_mapping.py
tests/test_merlin_io.py
tests/test_pets_input.py
tests/test_tools.py
tests/test_utils.py
tests/utils.py
tests/config/defaults.yaml
tests/config/settings.yaml
tests/config/calibration/calib_stage_rotation.yaml
tests/config/calibration/test.yaml
tests/config/camera/test.yaml
tests/config/microscope/test.yaml