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====== Recommended literature ======

This section lists recommended articles, review papers and books that will help users to gain a more detailed insight into the microscopy techniques available at the OICE.

===== Fluorophores =====
  * {{:1994-electronic_structure_of_the_excited_states_and_phenol_fluorescence.pdf|}}
  * {{:2004-photoswitchable_cyan_fluorescent_protein_for_protein_tracking.pdf|}}
  * {{:2006-engineering_of_a_monomeric_green-to-red.pdf|}}
  * {{:2007-advances_in_fluorescent_protein_technology.pdf|}}
  * {{:2008-lifeact_a_versatile_marker_to_visualize_f-actin.pdf|}}
  * {{:2009-a_bright_and_photostable_photoconvertible_fluorescent_protein_.pdf|}}
  * {{:2009-a_bright_and_photostable_photoconvertible_fluorescent_protein_1.pdf|}}
  * {{:2009-characterization_of_an_orange_acceptor_fluorescent_protein_for_sensitized_spectral_fluorescence_resonance_energy_transfer_microscopy_using_a_white-light_laser.pdf|}}
  * {{:2009-chem_soc_rev_reviewing_the_latest_developements_in_the_science_of_green_fluorescent_protein.pdf|}}
  * {{:2009-evaluating_and_improving_the_photostability_of_fluorescent_proteins.pdf|}}
  * {{:2009-excited_state_reactions_in_fluorescent_proteins.pdf|}}
  * {{:2009-genetically_encoded_biosensors_based_on_engineered_fluorescent_proteins.pdf|}}
  * {{:2009-photoactivatable_mcherry_for_high-resolution_two-color_1.pdf|}}
  * {{:2009-photoreactions_and_dynamics_of_the_green_fluorescent_protein.pdf|}}
  * {{:2009-stimulated_emission_depletion_nanoscopy_of_living_cells_using_snap-tag_fusion_proteins.pdf|}}
  * {{:2009-the_fluorescent_protein_palette_tools_for_cellular_imaging.pdf|}}
  * {{:2009-the_photochemistry_of_fluorescent_proteins_implications_for_their_biological_applications_.pdf|}}
  * {{:2002-two-photon_fluorescence_absorption_and_emission_spectra_of_dyes_relevant_for_cell_imaging.pdf|}}


===== Quality Assesssment =====
   *{{:2001-quantitative_comparison_of_anti-fading_mounting_media_for_confocal_laser_scanning_microscopy.pdf|}}
   *{{:2011-measuring_and_interpreting_point_spread_functions_to_determine_confocal_microscope_resolution_and_ensure_quality_control.pdf|}}
   *{{:2011-quality_assurance_testing_for_modern_optical_imaging_systems.pdf|}}
   *{{:2011-some_secrets_of_fluorescent_proteins_distinct_bleaching_in_various_mounting_fluids_and_photoactivation_of_cyan_fluorescent_proteins_at_yfp-excitation.pdf|}}
   *{{:2013-international_test_results_for_objective_lens_quality_resolution_spectral_accuracy_and_spectral_separation_for_confocal_laser_scanning_microscopes.pdf|}}
   *{{:1997-contrast_resolution_pixelation_dynamic_range_and_signal-to-noise_ratio_fundamental_limits_to_resolution_in_fluorescence_light_microscopy.pdf|}}


===== Confocal microscopy =====

===== Super Resolution =====
   *{{::1992-near-field_optics_microscopy_spectroscopy_and_surface_modification_beyond_the_diffraction_limit.pdf|}}
   *{{:2005-superresolution_by_localization_of_quantum_dots_using_blinking_statistics.pdf|}}
   *{{:2009-interferometric_fluorescent_super-resolution_microscopy_resolves_3d_cellular_ultrastructure.pdf|}}
   *{{:2010-a_guide_to_super-resolution_fluorescence_microscopy.pdf|}}
   *{{:2011-diffraction-unlimited_all-optical_imaging_and_writing_with_a_photochromic_gfp.pdf|}}
   *{{:2013-sted_microscopy_of_living_cells--new_frontiers_in_membrane_and_neurobiology.pdf|}}
   *{{:2014-eight_years_of_single-molecule_localization_microscopy.pdf|}}


 
===== Multi-Photon Intravital =====
  * {{:2005-deep_tissue_two-photon_microscopy.pdf|}}
  * {{:2005-looking_and_listening_to_light_the_evolution_of_whole-body_photonic_imaging.pdf|}}
  * {{:2008-imaging_in_the_era_of_molecular_oncology.pdf|}}
  * {{:2013-single-molecule_imaging_in_vivo_the_dancing_building_blocks_of_the_cell.pdf|}}
  * {{:2013-whole-body_imaging_of_adoptively_transferred_t_cells_using_magnetic_resonance_imaging_single_photon_emission_computed_tomography_and_positron_emission_tomography_techniques_with_a_focus_on_regulatory_t_cells.pdf|}}
  * {{:2014-advances_in_whole-embryo_imaging_a_quantitative_transition_is_underway.pdf|}}


===== Image Analysis =====
  * {{:2011-comparison_of_parameter-adapted_segmentation_methods_for_fluorescence_micrographs.pdf|}}
  * {{:2013-approaches_to_automatic_parameter_fitting_in_a_microscopy_image_segmentation_pipeline_an_exploratory_parameter_space_analysis.pdf|}}
  * {{:2014-review_of_free_software_tools_for_image_analysis_of_fluorescence_cell_micrographs.pdf|}}
  * {{:adaptive_color_spaces_based_on_multivariante_gaussian_distributions_for_color_image_segmentation.pdf|}}
  * {{:using_multimodal_information_for_the_segmentation_of_fluorescent_micrographs_with_application_to_virology_and_microbiology.pdf|}}
  * {{::2006-a_guided_tour_into_subcellular_colocalization_analysis_in_light_microscopy.pdf|}}
  * {{:2016_accurate_quantitative_wide-field_fluorescence.pdf|}}


 
===== FRET =====
  * {{:1998-quantitative_fluorescence_resonance_energy_transfer_measurements_using_fluorescence_microscopy.pdf|}}
  * {{:1999-gfp-based_fret_microscopy_in_living_plant_cells.pdf|}}
  * {{:2001-preassociation_of_calmodulin_with_voltage-gated_ca_2_channels_revealed_by_fret_in_single_living_cells.pdf|}}
  * {{:2001-reliable_and_global_measurement_of_fluorescence_resonance_energy_transfer_using_fluorescence_microscopes.pdf|}}
  * {{:2002-fluorescence_resonance_energy_transfer-based_stoichiometry_in_living_cells.pdf|}}
  * {{:2003-fluorescence_resonance_energy_transfer_fret_microscopy_imaging_of_live_cell_protein_localizations.pdf|}}
  * {{:2004-eosfp_a_fluorescent_marker_protein_with_uv-inducible_green-to-red_fluorescence_conversion.pdf|}}
  * {{:2006-fanciful_fret.pdf|}}
  * {{:2006-gfp-based_fret_analysis_in_live_cells.pdf|}}
  * {{:2006-rapid_metabolism_of_glucose_detected_with_fret_glucose_nanosensors_in_epidermal_cells_and_intact_roots_of_arabidopsis_rna-silencing_mutants.pdf|}}
  * {{:2008-combination_of_novel_green_fluorescent_protein_mutant_tsapphire_and_dsred_variant_morange_to_set_up_a_versatile_in_planta_fret-flim_assay.pdf|}}
  * {{:2009-fretting_about_fret_failure_of_the_ideal_dipole_approximation.pdf|}}
  * {{:2009-novel_lambda_fret_spectral_confocal_microscopy_imaging_method.pdf|}}
  * {{:2010-three-color_spectral_fret_microscopy_localizes_three_interacting_proteins_in_living_cells.pdf|}}
  * {{:2012fluorescent_proteins_for_fret_microscopy_monitoring_protein_interactions_in_living_cells.pdf|}}
  * {{:2012-fret_microscopy_in_the_living_cell_different_approaches_strengths_and_weaknesses.pdf|}}
  * {{:microscopic_analysis_of_fluorescence_resonance_energy_transfer_fret_.pdf|}}
  * {{:the_characterization_of_optimized_fluorescent_proteins_for_foerster_resonance_energy_transfer_microscopy.pdf|}}


===== FRAP =====
  * {{:1999-photobleaching_gfp_reveals_protein_dynamics_inside_live_cells.pdf|}}
  * {{:2000-diffusion_in_inhomogeneous_media_theory_and_simulations_applied_to_whole_cell_photobleach_recovery.pdf|}}
  * {{:2001-from_fixed_to_frap_measuring_protein_mobility_and_activity_in_living_cells.pdf|}}
  * {{:2001-kinetic_modelling_approaches_to_in_vivo_imaging.pdf|}}
  * {{:2002-using_frap_and_mathematical_modeling_to_determine_the_in_vivo_kinetics_of_nuclear_proteins.pdf|}}
  * {{:2004-challenges_and_artifacts_in_quantitative_photobleaching_experiments.pdf|}}
  * {{:2004-nucleocytoplasmic_shuttling_revealed_by_frap_and_flip_technologies.pdf|}}
  * {{:2005-frap_analysis_of_binding_proper_and_fitting.pdf|}}
  * {{:2005-systematic_evaluation_of_frap_experiments_performed_in_a_confocal_laser_scanning_microscope.pdf|}}

  
===== BiFC =====
  * {{:2003-simultaneous_visualization_of_multiple_protein_interactions_in_living_cells_using_multicolor_fluorescence_complementation_analysis.pdf|}}
  * {{:2006-design_and_implementation_of_bimolecular_fluorescence_complementation_bifc_assays_for_the_visualization_of_protein_interactions_in_living_cells.pdf|}}
  * {{:2006-visualization_of_molecular_interactions_by_fluorescence_complementation.pdf|}}
  * {{:2009-visualization_of_molecular_interactions_using_bimolecular_fluorescence_complementation_analysis_characteristics_of_protein_fragment_complementation.pdf|}}

  
===== General biology =====
  * {{:1998-hematopoietic_progenitor_cell_rolling_in_bone_marrow_microvessels_parallel_contributions_by_endothelial_selectins_and_vascular_cell_adhesion_molecule_1.pdf|}}
  * {{:2001-studying_protein_dynamics_in_living_cells.pdf|}}
  * {{:2005-cell_migration_at_a_glance.pdf|}}
  * {{:2008-interstitial_leukocyte_migration_and_immune_function.pdf|}}
  * {{:2009-collective_cell_migration_in_morphogenesis_regeneration_and_cancer.pdf|}}
  * {{:2010-cell_adhesion_integrating_cytoskeletal_dynamics_and_cellular_tension.pdf|}}
  * {{:2010-nuclear_mechanics_during_cell_migration.pdf|}}
  * {{:2011-two-photon_laser-generated_microtracks_in_3d_collagen_lattices_principles_of_mmp-dependent_and_-independent_collective_cancer_cell_invasion.pdf|}}
  * {{:2013-resolution_of_inflammation_an_integrated_view.pdf|}}

  

===== Lecture PDFs =====