Overview gallery - galizia-lab/pyview GitHub Wiki

This page illustrates the effect of different Overview flags on the overview generated, using synthetic data.

TIP: Click on flag names in blue color to read further usage information about the flag.

Contents

Colorbar Flags

Adding a scalebar

FakeData_raw666_00_no_scalebar FakeData_raw666_00_defaults
SO_xgap=0, CTV_scalebar=0 SO_xgap=30, CTV_scalebar=1

Scaling Flags

Scale data between maximum and minimum of all data

FakeData_raw666_00_defaults FakeData_raw666_00SO_individualScale2
SO_xgap=30, SO_individualScale=0, CTV_scalebar=1, SO_MV_scalemin=0, SO_MV_scalemax=1 SO_xgap=30, SO_individualScale=2, CTV_scalebar=1,SO_MV_scalemin=0, SO_MV_scalemax=1

Scale data between 20th percentile and 80th percentile of all data

FakeData_raw666_00_defaults FakeData_raw666_00SO_individualScale2_percentileValue20
SO_xgap=30, SO_individualScale=0, CTV_scalebar=1, SO_percentileScale=0, SO_percentileValue=0 SO_xgap=30, SO_individualScale=2, CTV_scalebar=1, SO_percentileScale=1, SO_percentileValue=0.2

Scale data between minimum and maximum of a central rectangular region

FakeData_raw666_00_defaults FakeData_raw666_00SO_individualScale3_factor0p25
SO_xgap=30, SO_individualScale=0, CTV_scalebar=1, SO_indiScale3factor=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25

NOTE: Here as well, data can be scaled to be within a range of percentile values instead of being with minimum and maximum values as above. To do this, specify the flags SO_percentileScale and SO_percentileValue.

Scale data between user-specified lower limit and data dependent upper limit

FakeData_raw666_00_defaults FakeData_raw666_00SO_individualScale4
SO_xgap=30, SO_individualScale=0, CTV_scalebar=1,SO_MV_scalemin=0 SO_xgap=30, SO_individualScale=4, CTV_scalebar=1,SO_MV_scalemin=0

Others

Lower and upper limits for data scaling can be restricted to be with an area specified by a .area or .area.tif file by setting the flag SO_individualScale to 5 and 6. Please click on the flag name in the previous sentence for more info.

Place 0 at center, scale positive and negative values differently

FakeData_raw666_00SO_individualScale2 FakeData_raw666_00SO_individualScale12
SO_xgap=30, SO_individualScale=2, CTV_scalebar=1, SO_xgap=30, SO_individualScale=12, CTV_scalebar=1

NOTE: SO_individualScale = 13, 14, 15 and 16 have the same effect relative to SO_individualScale = 3, 4, 5 and 6

Place 0 at center, scale positive and negative values equally, changing data limits

FakeData_raw666_00SO_individualScale2 FakeData_raw666_00SO_individualScale22
SO_xgap=30, SO_individualScale=2, CTV_scalebar=1, SO_xgap=30, SO_individualScale=22, CTV_scalebar=1

NOTE: SO_individualScale = 23, 24, 25 and 26 have the same effect relative to SO_individualScale = 3, 4, 5 and 6

Filter Flags

Apply spatial filter

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00space_filter_3
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, Signal_FilterSpaceFlag=0, Signal_FilterSpaceSize=3 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, Signal_FilterSpaceFlag=1, Signal_FilterSpaceSize=3

Exclusion Flags

Exclude pixel from all sides of the movie frame

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_individualScale3_factor0p25_cutborder5
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_cutborder=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_cutborder=5

Rotation Flags

Rotate Clockwise 90 degrees

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_1
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=1

Rotate Clockwise 180 degrees

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_2
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=2

Rotate Clockwise 270 degrees

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_3
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=3

Flip horizontally and rotate Clockwise 90 degrees

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_4
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=4

Flip horizontally

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_5
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=5

Flip vertically and rotate Clockwise 90 degrees

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_6
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=6

Flip vertically

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_rotateImage_7
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_rotateImage=7

Thresholding Flags

Threshold on foto1, focussing on pixels in foto1 higher than 1000 and lower than 400

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_thresholdOn_foto1_vals_a1000a400_withinArea_False
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=none, SO_lowerThreshPositiveResps=a0, SO_upperThreshNegativeResps=a0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=foto1, SO_lowerThreshPositiveResps=a1000, SO_upperThreshNegativeResps=a400

Threshold on foto1, focussing on pixels in foto1 with values in top 50% and bottom 30%

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_thresholdOn_foto1_vals_r50r30_withinArea_False
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=none, SO_lowerThreshPositiveResps=a0, SO_upperThreshNegativeResps=a0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=foto1, SO_lowerThreshPositiveResps=r50, SO_upperThreshNegativeResps=r30

Threshold on overview frame, focussing on pixels in overview frame higher than 0.05 and lower than -0.05

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_thresholdOn_overview_vals_a0.05a-0.05_withinArea_False
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=none, SO_lowerThreshPositiveResps=a0, SO_upperThreshNegativeResps=a0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=overview, SO_lowerThreshPositiveResps=a0.05, SO_upperThreshNegativeResps=a-0.05

Threshold on foto1, focussing on pixels in overview frame in top 50% and bottom 30%

FakeData_raw666_00SO_individualScale3_factor0p25 FakeData_raw666_00SO_thresholdOn_overview_vals_r50r30_withinArea_False
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=none, SO_lowerThreshPositiveResps=a0, SO_upperThreshNegativeResps=a0 SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=overview, SO_lowerThreshPositiveResps=r50, SO_upperThreshNegativeResps=r30

Threshold on foto1, focussing on pixels in overview frame in top 50% and bottom 30%, additionally restricting focus to area in .area/.area.tif file

FakeData_raw666_00SO_individualScale3_factor0p25 !FakeData_raw666_00SO_thresholdOn_overview_vals_r50r30_withinArea_True
SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=none, SO_lowerThreshPositiveResps=a0, SO_upperThreshNegativeResps=a0, SO_withinArea=False SO_xgap=30, SO_individualScale=3, CTV_scalebar=1, SO_indiScale3factor=0.25, SO_thresholdOn=overview, SO_lowerThreshPositiveResps=r50, SO_upperThreshNegativeResps=r30, SO_withinArea=True

NOTE: SO_withinArea=True can also be used together with other thresholding above to restrict similarly the area of focus.

Annotation Color Flags

FakeData_raw666_00_defaults FakeData_raw666_00_bgColor_yellow_fg_color_red
SO_xgap=30, CTV_scalebar=1, SO_fgColor=w, SO_bgColor=k SO_xgap=30, CTV_scalebar=1, SO_fgColor=r, SO_bgColor=y

Note: See here for valid values for colors.

Flags for marking ROI/Area

Mark ROI from .roi file

FakeData_raw666_00_defaults FakeData_raw666_00animal_only_roi_showROIs1_cutborder5
CTV_scalebar=1, SO_showROIs=0 CTV_scalebar=1, SO_showROIs=11

Note: An appropriately named .roi file should be present in the "Coor" folder.

Mark ROI from .coor file

FakeData_raw666_00_defaults FakeData_raw666_00animal_coor_showROIs1
CTV_scalebar=1, SO_showROIs=0, RM_Radius=5 CTV_scalebar=1, SO_showROIs=10, RM_Radius=5

Notes:

  1. An appropriately named .coor file should be present in the "Coor" folder.
  2. The size of the squares are equal to the value of flag RM_Radius.
  3. If an appropriately named .area/.area.tif file is present, it will take precendence.

Remove overview and show ROIs in different colors from .roi file

FakeData_raw666_00_defaults FakeData_raw666_00animal_only_roi_showROIs4
CTV_scalebar=1, SO_showROIs=0 CTV_scalebar=1, SO_showROIs=21

Note: An appropriately named .roi file should be present in the "Coor" folder.

Mark Area from .area.tif file

FakeData_raw666_00_defaults FakeData_raw666_00showROIs5
CTV_scalebar=1, SO_showROIs=0 CTV_scalebar=1, SO_showROIs=15

Note: An appropriately named .area.tif file should be present in the "Coor" folder.