ThreeB 1.1

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### - a -

- A : DataForMCMC , SampledBackgroundData , SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2 , FitSpots
- a : SPair
- add_remove_opt_hess_inner_samples : FitSpots
- add_remove_opt_retries : FitSpots
- add_remove_opt_samples : FitSpots
- add_remove_tries : FitSpots
- allowed_area : FitSpots
- area_extra_radius : FitSpots
- arg : three_B
- ave : FitSpots

### - b -

- b : SPair
- base_variance : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- bg : ThreeBDialog
- blue : ClassicGlow
- blur_fwhm : EControlPanel
- blur_mu : FitSpots
- blur_sigma : FitSpots
- buttons : EControlPanel

### - c -

- c : Kahan , ThreeBDialog , ExportButtonListener , SomethingChanges
- canvas : EControlPanel
- closeButton : EControlPanel
- complete : EControlPanel
- completePanelConstraints_ : FloatSliderWithBox
- config : ThreeBRunner
- count_ : ThreeBDialog
- cp : ThreeBRunner
- critical_iterations : ThreeBGlobalConstants
- current_sample : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- current_sample_intensities : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- cutout_current_sample_intensities : SampledMultispot::GibbsSampler2
- cutout_pixel_intensities : SampledMultispot::GibbsSampler2
- cutout_spot_intensities : SampledMultispot::GibbsSampler2

### - d -

- data_for_h_mcmc : FitSpots
- data_for_t_mcmc : FitSpots
- delta_max : ConjugateGradientOnly< Size, Precision >
- die : JNIUserInterface
- diff_log_prob : SampledMultispot::SpotWithBackgroundMasked

### - e -

- env : JNIUserInterface
- exportButton : EControlPanel
- exportButtonColor : EControlPanel

### - f -

- f : FloatSliderWithBox::SliderChanged , FloatSliderWithBox::TextChanged , CloseButtonListener
- fatal : ThreeBRunner
- filename : EControlPanel , ThreeBRunner
- format : FloatSliderWithBox

### - g -

- g : ConjugateGradientOnly< Size, Precision >
- graphics : FitSpots
- green : ClassicGlow

### - h -

- h : ConjugateGradientOnly< Size, Precision >
- h_inner_samples : FitSpots
- h_outer_samples : FitSpots
- hess_log_prob : SampledMultispot::SpotWithBackgroundMasked

### - i -

- ims : FitSpots
- intensity_mu : FitSpots
- intensity_sigma : FitSpots
- iteration : FitSpots , StateParameters
- iterations : ConjugateGradientOnly< Size, Precision > , EControlPanel
- its : ThreeBRunner

### - l -

- label : FloatSliderWithBox
- limit : FitSpots
- linear_reconstruction : EControlPanel
- linesearch_epsilon : ConjugateGradientOnly< Size, Precision >
- linesearch_tolerance : ConjugateGradientOnly< Size, Precision >
- log_prob : SampledMultispot::SpotWithBackgroundMasked

### - m -

- main_cg_max_iterations : FitSpots
- main_passes : FitSpots
- main_samples : FitSpots
- mask : three_B , ThreeBRunner
- max : FloatSliderWithBox
- max_iterations : ConjugateGradientOnly< Size, Precision >
- max_motion : FitSpots
- min : FloatSliderWithBox
- minus_h : ConjugateGradientOnly< Size, Precision >
- mu_blur : SampledBackgroundData , DataForMCMC
- mu_brightness : SampledBackgroundData , DataForMCMC

### - n -

- new_g : ConjugateGradientOnly< Size, Precision >
- nframes : AdvancedDialog , ThreeBDialog
- npix : ThreeBDialog
- num_frames : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- num_pixels : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- number : FloatSliderWithBox
- NumParameters : SampledMultispot::SpotWithBackgroundMasked

### - o -

- O : SampledBackgroundData , SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- ok : AdvancedDialog
- old_g : ConjugateGradientOnly< Size, Precision >
- old_h : ConjugateGradientOnly< Size, Precision >
- old_x : ConjugateGradientOnly< Size, Precision >
- outer_loop_iterations : FitSpots

### - p -

- pass : StateParameters
- passes : JNIUserInterface
- pi : SampledBackgroundData , FitSpots , DataForMCMC , SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- pixel_intensities : DataForMCMC , SampledBackgroundData , FitSpots , SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- pixel_size_in_nm : EControlPanel
- pixels : SampledBackgroundData , DataForMCMC , FitSpots , StateParameters , ThreeBRunner
- position_prior : FitSpots
- pts : EControlPanel

### - r -

- reciprocal : FloatSliderWithBox
- reconstructed_pixel_size : EControlPanel
- reconstruction_blur_fwhm : EControlPanel
- red : ClassicGlow
- rng : FitSpots , MT19937 , StateParameters , DataForMCMC
- roi : EControlPanel

### - s -

- sample_intensities_without_spot : SampledBackgroundData
- sample_iterations : DataForMCMC , SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2 , FitSpots
- samples : DataForMCMC
- save_spots : FitSpots
- scale_brightness_limit : FitSpots
- Second : IndexLexicographicPosition< Cmp, First >
- send_message_string : JNIUserInterface
- send_new_points : JNIUserInterface
- should_stop : JNIUserInterface
- sigma_blur : DataForMCMC , SampledBackgroundData
- sigma_brightness : SampledBackgroundData , DataForMCMC
- size : ConjugateGradientOnly< Size, Precision >
- slider : FloatSliderWithBox
- spot_intensities : SampledMultispot::GibbsSampler , SampledMultispot::GibbsSampler2
- spot_pixels : SampledMultispot::GibbsSampler2
- spots : IndexLexicographicPosition< Cmp, First > , SampledMultispot::GibbsSampler , StateParameters , SampledMultispot::GibbsSampler2 , FitSpots
- start_iteration : FitSpots
- start_pass : FitSpots
- start_time : ThreeBRunner
- status : EControlPanel
- steps : FloatSliderWithBox
- stop : ThreeBRunner
- stopButton : EControlPanel
- stopped : ThreeBRunner
- sum : Kahan

### - t -

- t : Kahan , StopButtonListener
- tbr : EControlPanel
- text : FloatSliderWithBox
- ThreeBRunner_this : JNIUserInterface
- time_cg : FitSpots
- time_gibbs : FitSpots
- time_msg : EControlPanel
- tolerance : ConjugateGradientOnly< Size, Precision >
- tsamples : FitSpots

### - u -

- ui : FitSpots
- units : FloatSliderWithBox
- use_position_prior : FitSpots

### - v -

- value : FloatSliderWithBox
- variance : SampledMultispot::GibbsSampler2 , SampledMultispot::GibbsSampler , FitSpots , SampledBackgroundData , DataForMCMC

### - w -

- what : LogFileParseError
- window : three_B

### - x -

- x : ConjugateGradientOnly< Size, Precision > , Spot

### - y -

- y : Kahan , Spot

### - z -

- zoom : EControlPanel