_ApplyBinRestrictionToFFT, _Deconv_2DDeconvolution, _Deconv_2DFastDeconvolution, _Deconv_3DDeconvolution, _Deconv_Automatic, _Deconv_ExtractPSF, _FourierTransform2D, _InverseFourierTransform2D, _PowerSpectrum2D, ApplyBinRestrictionToFFT, ApplyBinRestrictionToFFT_ND, Deconv_2DAutoDeconvolution, Deconv_2DBlindDeconvolution, Deconv_2DFastDeconvolution, Deconv_2DLandweberDeconvolution, Deconv_2DLucyRichardsonDeconvolution, Deconv_3DAutoDeconvolution, Deconv_3DBlindDeconvolution, Deconv_3DFastDeconvolution, Deconv_3DLandweberDeconvolution, Deconv_3DLucyRichardsonDeconvolution, Deconv_Live, Deconv_LiveDeBlurSetParameters, Deconv_LiveDeBlurSetRectangle, Deconv_LiveDeBlurSetupToggle, Deconv_LiveDeBlurShowGUI, Deconv_LiveDeBlurSwitch, FourierTransform2D, FourierTransform2D_ND, InverseFourierTransform2D, InverseFourierTransform2D_ND, PowerSpectrum2D, PowerSpectrum2D_ND

ApplyBinRestrictionToFFT

Interactive command to this function: Image > Fourier Transform > Apply Binary Mask on FT

Description 

 ApplyBinRestrictionToFFT();

Applies binary mask on the Fourier transform image.

ApplyBinRestrictionToFFT_ND

Description 

 ApplyBinRestrictionToFFT_ND(
   int  NDTLoop,
   int  NDMPLoop,
   int  NDZLoop
);

Applies binary mask on the specified dimension of the Fourier Transform image.

Parameters

int NDTLoop

0	apply to the current loop only
1	apply to the whole Time dimension

int NDMPLoop

Apply to Multi Point dimension.

0	apply to the current loop only
1	apply to the whole Multi Point dimension

int NDZLoop

Apply to Z dimension

0	apply to the current loop only
1	apply to the whole Z Series dimension

Deconv_2DAutoDeconvolution

Description 

 Deconv_2DAutoDeconvolution(
   double  XDDec_NA,
   double  XDDec_RI,
   int  FastSubBackgnd,
   char *XDDec_SubBackVal,
   int  XDDec_Modality,
   double  XDDec_Calib,
   double  XDDec_PinholeSize,
   int  XDDec_SlitOrientation,
   double  XDDec_RealMag,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   char *XDDec_Filename,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   int  DecRemoveSpuriousPixels
);

Performs Automatic 2D Deconvolution.

Parameters

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

int FastSubBackgnd

Apply background subtraction?

0	no
1	yes

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_Calib

Image calibration.

double XDDec_PinholeSize

Pinhole size.

int XDDec_SlitOrientation

Swept-field confocal slit orientation.

0	vertical
1	horizontal

double XDDec_RealMag

Magnification.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_2DBlindDeconvolution

Description 

 Deconv_2DBlindDeconvolution(
   double  XDDec_NA,
   double  XDDec_RI,
   int  XDDec_SNR,
   int  FastSubBackgnd,
   char *XDDec_SubBackVal,
   int  XDDec_Modality,
   double  XDDec_Calib,
   double  XDDec_PinholeSize,
   int  XDDec_SlitOrientation,
   double  XDDec_RealMag,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   char *XDDec_Filename,
   int  DecIterations,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   int  DecRemoveSpuriousPixels
);

Performs the 2D Blind Deconvolution of the current image.

Parameters

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int FastSubBackgnd

Apply background subtraction?

0	no
1	yes

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_Calib

Image calibration.

double XDDec_PinholeSize

Pinhole size.

int XDDec_SlitOrientation

Swept-field confocal slit orientation.

0	vertical
1	horizontal

double XDDec_RealMag

Magnification.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

int DecIterations

Number of iterations.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_2DFastDeconvolution

Description 

 Deconv_2DFastDeconvolution(
   double  XDDec_NA,
   double  XDDec_RI,
   int  XDDec_SNR,
   int  FastSubBackgnd,
   char *XDDec_SubBackVal,
   int  XDDec_Modality,
   double  XDDec_Calib,
   double  XDDec_PinholeSize,
   int  XDDec_SlitOrientation,
   double  XDDec_RealMag,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   char *XDDec_Filename,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   int  DecRemoveSpuriousPixels
);

This function performs 2D Fast Deconvolution on the image.

Parameters

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int FastSubBackgnd

Apply background subtraction?

0	no
1	yes

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_Calib

Image calibration.

double XDDec_PinholeSize

Pinhole size.

int XDDec_SlitOrientation

Swept-field confocal slit orientation.

0	vertical
1	horizontal

double XDDec_RealMag

Magnification.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

See Also 
Deconv_2DBlindDeconvolution

Deconv_2DLandweberDeconvolution

Description 

 Deconv_2DLandweberDeconvolution(
   double  XDDec_NA,
   double  XDDec_RI,
   int  XDDec_SNR,
   int  FastSubBackgnd,
   char *XDDec_SubBackVal,
   int  XDDec_Modality,
   double  XDDec_Calib,
   double  XDDec_PinholeSize,
   int  XDDec_SlitOrientation,
   double  XDDec_RealMag,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   char *XDDec_Filename,
   int  DecIterations,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   int  DecRemoveSpuriousPixels
);

Performs the 2D Landweber Deconvolution of the current ND image.

Parameters

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int FastSubBackgnd

Apply background subtraction?

0	no
1	yes

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_Calib

Image calibration.

double XDDec_PinholeSize

Pinhole size.

int XDDec_SlitOrientation

Swept-field confocal slit orientation.

0	vertical
1	horizontal

double XDDec_RealMag

Magnification.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

int DecIterations

Number of iterations.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_2DLucyRichardsonDeconvolution

Description 

 Deconv_2DLucyRichardsonDeconvolution(
   double  XDDec_NA,
   double  XDDec_RI,
   int  XDDec_SNR,
   int  FastSubBackgnd,
   char *XDDec_SubBackVal,
   int  XDDec_Modality,
   double  XDDec_Calib,
   double  XDDec_PinholeSize,
   int  XDDec_SlitOrientation,
   double  XDDec_RealMag,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   char *XDDec_Filename,
   int  DecIterations,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   int  DecRemoveSpuriousPixels
);

Performs the 2D Richardson-Lucy Deconvolution of the current ND image.

Parameters

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int FastSubBackgnd

Apply background subtraction?

0	no
1	yes

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_Calib

Image calibration.

double XDDec_PinholeSize

Pinhole size.

int XDDec_SlitOrientation

Swept-field confocal slit orientation.

0	vertical
1	horizontal

double XDDec_RealMag

Magnification.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

int DecIterations

Number of iterations.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_3DAutoDeconvolution

Description 

 Deconv_3DAutoDeconvolution(
   int  XDDec_Modality,
   double  XDDec_PinholeSize,
   double  XDDec_NA,
   double  XDDec_RI,
   double  XDDec_Calib,
   double  XDDec_ZStep,
   char *XDDec_Filename,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   double  XDDec_RealMag,
   char *XDDec_FXYZTXYZ,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   double  XDDec_DepthBelowCoverslip,
   double  XDDec_SampleRI,
   int  DecRemoveSpuriousPixels
);

Performs Automatic 3D Deconvolution of the current ND image.

Parameters

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_PinholeSize

Pinhole size.

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

double XDDec_Calib

Image calibration.

double XDDec_ZStep

Z-step size.

char *XDDec_Filename

Name of an imported file which contains point-spread function.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

double XDDec_RealMag

Magnification.

char *XDDec_FXYZTXYZ

Bounds of the rectangle used as a Region of Interest.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

double XDDec_DepthBelowCoverslip

Depth below coverslip.

double XDDec_SampleRI

Sample refractive index.

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_3DBlindDeconvolution

Description 

 Deconv_3DBlindDeconvolution(
   int  XDDec_Modality,
   double  XDDec_PinholeSize,
   double  XDDec_NA,
   double  XDDec_RI,
   double  XDDec_Calib,
   double  XDDec_ZStep,
   int  XDDec_Iteration,
   char *XDDec_Filename,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   double  XDDec_RealMag,
   int  XDDec_SubBackgnd,
   int  XDDec_SNR,
   char *XDDec_FXYZTXYZ,
   char *XDDec_SubBackVal,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   double  XDDec_DepthBelowCoverslip,
   double  XDDec_SampleRI,
   int  DecRemoveSpuriousPixels
);

Performs the 3D Blind Deconvolution of the current ND image.

Parameters

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_PinholeSize

Pinhole size.

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

double XDDec_Calib

Image calibration.

double XDDec_ZStep

Z-step size.

int XDDec_Iteration

Number of iterations.

0	Automatic count

char *XDDec_Filename

Name of an imported file which contains point-spread function.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

double XDDec_RealMag

Magnification.

int XDDec_SubBackgnd

Background subtraction.

-1	Automatic background estimation + subtraction
0	no subtraction
1	yes, subtract XDDec_SubBackVal

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

char *XDDec_FXYZTXYZ

Bounds of the rectangle used as a Region of Interest.

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

double XDDec_DepthBelowCoverslip

Depth below coverslip.

double XDDec_SampleRI

Sample refractive index.

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

See Also 
Deconv_2DBlindDeconvolution

Deconv_3DFastDeconvolution

Description 

 Deconv_3DFastDeconvolution(
   int  XDDec_Modality,
   double  XDDec_PinholeSize,
   double  XDDec_NA,
   double  XDDec_RI,
   double  XDDec_Calib,
   double  XDDec_ZStep,
   int  XDDec_Iteration,
   char *XDDec_Filename,
   char *XDDec_Mask,
   char *XDDec_Wave,
   int  XDDec_SNR,
   char *XDDec_WaveExc,
   double  XDDec_RealMag,
   int  XDDec_SubBackgnd,
   char *XDDec_FXYZTXYZ,
   char *XDDec_SubBackVal,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   double  XDDec_DepthBelowCoverslip,
   double  XDDec_SampleRI,
   int  DecRemoveSpuriousPixels
);

Performs the 3D Fast Deconvolution of the current ND image.

Parameters

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_PinholeSize

Pinhole size.

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

double XDDec_Calib

Image calibration.

double XDDec_ZStep

Z-step size.

int XDDec_Iteration

Number of iterations.

0	Automatic count

char *XDDec_Filename

Name of an imported file which contains point-spread function.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

char *XDDec_WaveExc

Channel excitation wavelength.

double XDDec_RealMag

Magnification.

int XDDec_SubBackgnd

Background subtraction.

-1	Automatic background estimation + subtraction
0	no subtraction
1	yes, subtract XDDec_SubBackVal

char *XDDec_FXYZTXYZ

Bounds of the rectangle used as a Region of Interest.

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

double XDDec_DepthBelowCoverslip

Depth below coverslip.

double XDDec_SampleRI

Sample refractive index.

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

See Also 
Deconv_3DBlindDeconvolution

Deconv_3DLandweberDeconvolution

Description 

 Deconv_3DLandweberDeconvolution(
   int  XDDec_Modality,
   double  XDDec_PinholeSize,
   double  XDDec_NA,
   double  XDDec_RI,
   double  XDDec_Calib,
   double  XDDec_ZStep,
   int  XDDec_Iteration,
   char *XDDec_Filename,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   double  XDDec_RealMag,
   int  XDDec_SNR,
   int  XDDec_SubBackgnd,
   char *XDDec_FXYZTXYZ,
   char *XDDec_SubBackVal,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   double  XDDec_DepthBelowCoverslip,
   double  XDDec_SampleRI,
   int  DecRemoveSpuriousPixels
);

Performs the 3D Landweber Deconvolution of the current ND image.

Parameters

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_PinholeSize

Pinhole size.

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

double XDDec_Calib

Image calibration.

double XDDec_ZStep

Z-step size.

int XDDec_Iteration

Number of iterations.

0	Automatic count

char *XDDec_Filename

Name of an imported file which contains point-spread function.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

double XDDec_RealMag

Magnification.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int XDDec_SubBackgnd

Background subtraction.

-1	Automatic background estimation + subtraction
0	no subtraction
1	yes, subtract XDDec_SubBackVal

char *XDDec_FXYZTXYZ

Bounds of the rectangle used as a Region of Interest.

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

double XDDec_DepthBelowCoverslip

Depth below coverslip.

double XDDec_SampleRI

Sample refractive index.

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_3DLucyRichardsonDeconvolution

Description 

 Deconv_3DLucyRichardsonDeconvolution(
   int  XDDec_Modality,
   double  XDDec_PinholeSize,
   double  XDDec_NA,
   double  XDDec_RI,
   double  XDDec_Calib,
   double  XDDec_ZStep,
   int  XDDec_Iteration,
   char *XDDec_Filename,
   char *XDDec_Mask,
   char *XDDec_Wave,
   char *XDDec_WaveExc,
   double  XDDec_RealMag,
   int  XDDec_SNR,
   int  XDDec_SubBackgnd,
   char *XDDec_FXYZTXYZ,
   char *XDDec_SubBackVal,
   int  XDDec_NewDocument,
   int  XDDec_HigherBitDepthDocument,
   double  XDDec_DepthBelowCoverslip,
   double  XDDec_SampleRI,
   int  DecRemoveSpuriousPixels
);

Performs the 3D Richardson-Lucy Deconvolution of the current ND image.

Parameters

int XDDec_Modality

Microscope modality.

1	Wide field
2	Point scan confocal
3	SFC/Pinhole mode
4	SFC/Slit mode
5	Spinning disc
6	DSD confocal
7	Two photon
8	NSIM
9	NSPARC / Reassign
10	NSPARC / Sum
11	iSIM
12	RCM
13	CSU W1-SoRa

double XDDec_PinholeSize

Pinhole size.

double XDDec_NA

Numerical aperture value.

double XDDec_RI

Refraction index of the immersion medium.

double XDDec_Calib

Image calibration.

double XDDec_ZStep

Z-step size.

int XDDec_Iteration

Number of iterations.

0	Automatic count

char *XDDec_Filename

Name of an imported file which contains point-spread function.

char *XDDec_Mask

Which channels are deconvolved.

0	leave channel
1	deconvolve channel

char *XDDec_Wave

Channel emission wavelength.

char *XDDec_WaveExc

Channel excitation wavelength.

double XDDec_RealMag

Magnification.

int XDDec_SNR

Signal to noise ratio reasonably ranging from 10 (noisy image) to 50 (image almost without noise). The conversion table between “noise level” values and SNR values follows:

Clear	50
Low Noise	31
Medium	26
Noisy	19
Grainy	12

int XDDec_SubBackgnd

Background subtraction.

-1	Automatic background estimation + subtraction
0	no subtraction
1	yes, subtract XDDec_SubBackVal

char *XDDec_FXYZTXYZ

Bounds of the rectangle used as a Region of Interest.

char *XDDec_SubBackVal

Value for background subtraction.

int XDDec_NewDocument

Creates a new document.

0	New document is not created.
1	New document is created.

int XDDec_HigherBitDepthDocument

Increase bit-depth of the resulting image?

0	Keep original bit-depth.
1	Increase bit-depth to 16 bit per channel.
2	Convert to “floating point image” (pixel values are floating-point numbers )

double XDDec_DepthBelowCoverslip

Depth below coverslip.

double XDDec_SampleRI

Sample refractive index.

int DecRemoveSpuriousPixels

If dark artifacts occur in the deconvolved image, it could be caused by single high intensity pixels which are sometimes produced by a confocal scanner. This parameter turns on the “Remove spurious high intensity pixels” filter ON/OFF which removes these pixels from the image before deconvolution.

0	Leave the image unchanged.
1	Remove spurious high intensity pixels before deconvolution.

Deconv_Live

This function runs the Deconvolution > Deconvolution > Live Denoise & Deconvolution command.

Description 

 Deconv_Live();

Opens the Live Denoise & Deconvolution dialog window.

Deconv_LiveDeBlurSetParameters

Description 

 Deconv_LiveDeBlurSetParameters(
   int  LiveDecParameterPSF,
   int  LiveDecParamNoise,
   int  LiveDecParamContrast,
   int  LiveDecParamSubBack
);

This function sets initial parameters for the Live De-blur algorithm. The parameters correspond to the settings in the Live De-Blur window.

Parameters

int LiveDecParameterPSF

Specimen thickness.

0	Thin
1	Normal
2	Thick

int LiveDecParamNoise

The amount of noise present in the image.

0	Clear
1	Normal
2	Noisy

int LiveDecParamContrast

Enhance contrast in the resulting image?

0	No contrast enhancement
1	Low contrast enhancement
2	Medium contrast enhancement
3	Strong contrast enhancement

int LiveDecParamSubBack

Background subtraction.

0	no
1	yes

Deconv_LiveDeBlurSetRectangle

Description 

 Deconv_LiveDeBlurSetRectangle(
   int  LiveDecRectLeft,
   int  LiveDecTop,
   int  LiveDecRectRight,
   int  LiveDecRectBottom
);

This function specifies a rectangular area where the Live De-Blur will be performed (when turned ON).

Parameters

int LiveDecRectLeft

X coordinate of the top left corner of the rectangle from the image origin (also top left corner).

int LiveDecTop

Y coordinate of the top left corner of the rectangle from the image origin.

int LiveDecRectRight

X coordinate of the bottom right corner of the rectangle from the image origin.

int LiveDecRectBottom

Y coordinate of the bottom right corner of the rectangle from the image origin.

Deconv_LiveDeBlurSetupToggle

This function runs the Deconvolution > Deconvolution > Show Live De-Blur Setup command.

Description 

 Deconv_LiveDeBlurSetupToggle();

This function toggles visibility of the Live De-Blur control window.

Deconv_LiveDeBlurShowGUI

Description 

 Deconv_LiveDeBlurShowGUI(
   int  LiveDecShowGUI
);

Opens or hides the Live De-Blur control window.

Parameters

int LiveDecShowGUI

0	Hide the window.
1	Show the window.

Deconv_LiveDeBlurSwitch

Description 

 Deconv_LiveDeBlurSwitch(
   int  LiveDecSwitch
);

Turns the Live De-Blur functionality ON/OFF.

Parameters

int LiveDecSwitch

Turn the De-Blur On/Off.

0	Stop Live De-Blur
1	Run Live De-Blur

FourierTransform2D

Interactive command to this function: Image > Fourier Transform > Forward 2D Fourier Transform

Description 

 FourierTransform2D();

Performs Forward Fourier Transform.

FourierTransform2D_ND

Description 

 FourierTransform2D_ND(
   int  NDTLoop,
   int  NDMPLoop,
   int  NDZLoop
);

Performs Forward Fourier Transform on the specified dimension of the ND file.

Parameters

int NDTLoop

0	apply to the current loop only
1	apply to the whole Time dimension

int NDMPLoop

Apply to Multi Point dimension.

0	apply to the current loop only
1	apply to the whole Multi Point dimension

int NDZLoop

Apply to Z dimension

0	apply to the current loop only
1	apply to the whole Z Series dimension

InverseFourierTransform2D

Interactive command to this function: Image > Fourier Transform > Inverse 2D Fourier Transform

Description 

 InverseFourierTransform2D();

Performs Inverse Fourier Transform 2D.

InverseFourierTransform2D_ND

Description 

 InverseFourierTransform2D_ND(
   int  NDTLoop,
   int  NDMPLoop,
   int  NDZLoop
);

Performs Inverse Fourier Transform 2D on the specified dimension of the ND file.

Parameters

int NDTLoop

0	apply to the current loop only
1	apply to the whole Time dimension

int NDMPLoop

Apply to Multi Point dimension.

0	apply to the current loop only
1	apply to the whole Multi Point dimension

int NDZLoop

Apply to Z dimension

0	apply to the current loop only
1	apply to the whole Z Series dimension

PowerSpectrum2D

Interactive command to this function: Image > Fourier Transform > Log Power Spectrum

Description 

 PowerSpectrum2D();

This function applies the 2D Fourier Transformation.

PowerSpectrum2D_ND

Description 

 PowerSpectrum2D_ND(
   int  NDTLoop,
   int  NDMPLoop,
   int  NDZLoop
);

This function applies the 2D Fourier Transformation on the current ND2 image.

Parameters

int NDTLoop

0	apply to the current loop only
1	apply to the whole Time dimension

int NDMPLoop

Apply to Multi Point dimension.

0	apply to the current loop only
1	apply to the whole Multi Point dimension

int NDZLoop

Apply to Z dimension

0	apply to the current loop only
1	apply to the whole Z Series dimension

_ApplyBinRestrictionToFFT

This function runs the Image > Fourier Transform > Apply Binary Mask on FT command.

Description 

 _ApplyBinRestrictionToFFT();

Applies binary mask on the Fourier transform image.

_Deconv_Automatic

Description 

 _Deconv_Automatic();

Performs automatic deconvolution on the currently opened image.

_Deconv_2DDeconvolution

This function runs the Deconvolution > Deconvolution > 2D Deconvolution command.

Description 

 _Deconv_2DDeconvolution();

This function displays the 2D Deconvolution window which sets the 2D deconvolution setting.

_Deconv_2DFastDeconvolution

Description 

 _Deconv_2DFastDeconvolution();

Opens the 2D Fast Deconvolution dialog window.

2D Fast Options

Specimen Thickness

Estimate thickness of the specimen: Flat, Thin, Normal, or Thick. This parameter influences the PSF shape.

Image Noise Level

Specify an estimation of the amount of noise present in the image.

Contrast enhancement

This option specifies whether contrast post-processing shall be performed after deconvolution. Choose its strength from the combo box.

Note

If you are not sure about its strength, select None. After the deconvolution is finished, you can use the Image > Contrast command instead.

Subtract background before deconvolution

If checked, the application subtracts the background value from the image before deconvolution.

Preview

Check this item to see the changes and the result immediately in the image.

Channels

Image channels produced by your camera are listed within this table. You can decide which channel(s) shall be processed by checking the check boxes next to the channel names. The emission wavelength value may be edited (except the Live De-Blur method).

Note

Brightfield channels are omitted automatically.

_Deconv_3DDeconvolution

This function runs the Deconvolution > Deconvolution > 3D Deconvolution command.

Description 

 _Deconv_3DDeconvolution();

This function displays the 3D Deconvolution window which sets the 3D deconvolution setting.

_Deconv_ExtractPSF

This function runs the Deconvolution > Deconvolution > Extract PSF command.

Description 

 _Deconv_ExtractPSF();

Opens a dialog for extracting PSF from the current image (containing captured beads). See the menu command description.

_FourierTransform2D

This function runs the Image > Fourier Transform > Forward 2D Fourier Transform command.

Description 

 _FourierTransform2D();

Opens the 2D Fourier Transformation dialog window.

_InverseFourierTransform2D

This function runs the Image > Fourier Transform > Inverse 2D Fourier Transform command.

Description 

 _InverseFourierTransform2D();

Opens the dialog window serving to recover a function from its Fourier transformation.

_PowerSpectrum2D

This function runs the Image > Fourier Transform > Log Power Spectrum command.

Description 

 _PowerSpectrum2D();

This function opens the 2D Fourier Transformation.