Artifact Correction Flags - galizia-lab/pyview GitHub Wiki
Artifact Correction of Raw Data
LE_BleachCorrMethod
What does it do?
This flag indicates the method for correcting bleaching artifacts.
Default value: None
What values can it take?
String values, Possible values:
- None: bleaching artifacts are not corrected
- log_uniform: fluorescence relative to background is assumed to follow the same exponential function for all pixels (all pixels of the image, or of the area given in an area file, depends on Flag LE_BleachExcludeArea).
- log_pixelwise_1cpu: fluorescence relative to background is assumed to follow different exponential functions for different pixels. Correction is done using only one CPU core
- log_pixelwise_parallel: the same as
log_pixelwise_1cpu, except correction is done in parallel using all CPU cores (currently fails with an error on Windows, works on Linux/Mac)
Are values expected to be in specific units?
No
Special Notes
None
LE_BleachCutBorder
What does it do?
This flag indicates the percentage of pixels to exclude along the border when not using AREA file.
Default value: 20
What values can it take?
Integer values
Are values expected to be in specific units?
Yes, number of pixels.
Special Notes
Noone
LE_BleachExcludeArea
What does it do?
If True, function fitting for bleach correction will exclude pixels outside AREA mask, if an appropriate AREA file is found
Default value: True
What values can it take?
Boolean values
Are values expected to be in specific units?
No
Special Notes
None
LE_BleachExcludeStimulus
What does it do?
If True, function fitting for bleach correction will exclude stimulus frames. Stimulus frames are defined to begin at the end of background and they end based on LELog_ExcludeSeconds.
Default value: True
What values can it take?
Boolean values
Are values expected to be in specific units?
No
Special Notes
None
LE_BleachStartFrame
What does it do?
This flag indicates the number of frames to exclude from the beginning of a measurement when fitting functions for bleach correction
Default value: 2
What values can it take?
Integer values
Are values expected to be in specific units?
Yes, number of frames
Special Notes
None
LELog_ExcludeSeconds
What does it do?
This flag indicates the number of seconds after the end of background to exclude when fitting functions for bleach correction
Default value: 0
What values can it take?
Integer values
Are values expected to be in specific units?
Yes, number of frames
Special Notes
None
LELog_InitialFactor
What does it do?
This flag indicates factor by which all frames up to the end of background are up-weighted when fitting functions for bleach correction
Default value: 1
What values can it take?
Float
Are values expected to be in specific units?
No
Special Notes
None
LE_ScatteredLightFactor
What does it do?
This flag indicates the strength of scattered light correction to be applied.
Default value: 0
What values can it take?
Float
- 0 turns off correction
- 1 applied full strength correction
Are values expected to be in specific units?
No
Special Notes
None
LE_ScatteredLightRadius
What does it do?
This flag indicates the radius of the scattered light correction to be applied in micrometers
Default value: 50
What values can it take?
Float
Are values expected to be in specific units?
yes, in micrometers
Special Notes
None
Data_Median_Filter
What does it do?
This flag indicates the way in which raw data should be filtered with a rolling window MEDIAN filter
Default value: 0
What values can it take?
One among the following integers:
- 0: no filter
- 1: filter in space with size 3, no time filter
- 2: filter in time with size 3, no space filter
- 3: filter in space and time, using flag values Data_Median_Filter_space and Data_Median_Filter_time
Are values expected to be in specific units?
no
Special Notes
None
Data_Median_Filter_space
What does it do?
This flag indicates the width of the MEDIAN filter used for filtering values over SPACE. Only used if Data_Median_Filter is set to 3.
Default value: 3
What values can it take?
Integers
Are values expected to be in specific units?
yes, in number of pixels
Special Notes
None
Data_Median_Filter_time
What does it do?
This flag indicates the width of the MEDIAN filter used for filtering values over TIME. Only used if Data_Median_Filter is set to 3.
Default value: 3
What values can it take?
Integers
Are values expected to be in specific units?
yes, in number of frames
Special Notes
None
Data_Mean_Filter
What does it do?
This flag indicates the way in which raw data should be filtered with a rolling window MEAN filter
Default value: 0
What values can it take?
One among the following integers:
- 0: no filter
- 1: filter in space with size 3, no time filter
- 2: filter in time with size 3, no space filter
- 3: filter in space and time, using flag values Data_Mean_Filter_space and Data_Mean_Filter_time
Are values expected to be in specific units?
no
Special Notes
None
Data_Mean_Filter_space
What does it do?
This flag indicates the width of the MEAN filter used for filtering values over SPACE. Only used if Data_Mean_Filter is set to 3.
Default value: 3
What values can it take?
Integers
Are values expected to be in specific units?
yes, in number of pixels
Special Notes
None
Data_Mean_Filter_time
What does it do?
This flag indicates the width of the MEAN filter used for filtering values over TIME. Only used if Data_Mean_Filter is set to 3.
Default value: 3
What values can it take?
Integers
Are values expected to be in specific units?
yes, in number of frames
Special Notes
None
Data_ReplaceInitFrames
What does it do?
When it is 2, the first two frames are replaced by the third right after reading data from file
Default value: 0 (no effect)
What values can it take?
Non negative Integers
Are values expected to be in specific units?
yes, in number of frames
Special Notes
None