https://imagej.net/ij/docs/menus/analyze.html
- Run CNN w/o transformations to see if accuracy increases
- Recap. the CNN code
- How we process the synthetic and experimental images
- Take experimental images and make them amenable to the CNN
- Divide toybox - complete
Cluster 0 = Mean 0 - images that no pattern
Cluster 1 = Mean 255 - complete coverage
Cluster 2 = Mean .006 - 189 - small spots
Cluster 3 = Mean 59.351 - 141.68 - long spots
Cluster 4 = 11.892 - 254.987 -
Cluster 5 = 110.332 - 252.66 -
Cluster 6 = 12.667 - 252.998 -
Ua - Degradation rate for NEGAN
Ui - Degradation rate for RTO
Ga - Self-activation of A by A
Gi - Activation of I by A
Ba - Inhibition of A by I
Da - Diffusion rate of A
Di - Diffusion rate of I
pattern - Classified manually. Either 1 or 0.
noise - 0 - 3693 with every integer in between being represented.
path - Path to the file
seed - ???. Ranges from 3-23352.
dir - Directory where the file is found
feat_bool - Feature boolean. ???.
num_spots - Number of spots
Mean - Mean coverage in the figure. Can range from 0 (completely blank) to 255 (completely filled)
Median - Median coverage in the figure. Can range from 0 (completely blank) to 255 (completely filled)
Area_mean - Average area of detected objects (maybe spots). Ranges from 1.0 to 40000.0. Max area is completely filled in. Grid is 200 by 200.
Area_std - Standard Deviation of area
X_mean - Average X coordinate of spots (?)
X_std - Standard deviation of X values
Y_mean - Average Y coordinates of spots (?)
Y_std - Standard deviation of Y values
Perim._mean - Mean of perimenter of spots
Perim._std - Standard deviation of perimeter of spots
BX_mean - ???
BX_std - ???
BY_mean - ???
BY_std - ???
Width_mean - Mean of spot width
Width_std - Spot width standard deviation
Height_mean - Mean height of spot
Height_std - Standard deviation of spot height
Major_mean - ???
Major_std - ???
Minor_mean - ???
Minor_std - ???
Angle_mean - Mean of an agle (what angle??)
Angle_std - Standard deviation of the mean ^^
Circ._mean - Mean of (???) circumference
Circ._std - Standard deviation of circumference
Feret_mean - Mean of feret diameter (distance between two parallel lines tangent to its boundary)
Feret_std - Standard deviation of feret diameter
IntDen_mean - Average integrated density (sum of pixel values) in object
IntDen_std - Standard deviation of integrated density
%Area_mean - ???
%Area_std - ???
RawIntDen_mean - Average raw intensity
RawIntDen_std - Raw intensity standard deviation. (Raw intensity = sum of all pixel areaas)
FeretX_mean - Mean X Coordinate of the feret
FeretX_std - Standard deviation of the X coordinate of the feret
FeretY_mean - Mean Y coordinate of the feret
FeretY_std - Standard deviation of the Y coordinate of the feret
FeretAngle_mean - Mean feret (?) angle
FeretAngle_std - Standard deviation of the feret angle
MinFeret_mean - Average minimum feret diameter
MinFeret_std - Minimum feret diameter standard deviation
AR_mean - Average aspect ratio
AR_std - Aspect ratio standard deviation (?)
Round_mean - Average roundness
Roundness = 4 · Area / (π · (Major axis)²))
Round_std - Roundness standard deviation
Solidity_mean - Average solidity (what is solidity?). Rnages from 0.4074 to 1.0.
Solidity_std - Solidity standard variation.
num_spots_inverted - Num_spots is inverted through some kind of function similair to a / (x + b) where a and b are constants.
Mean_inverted - Mean coverage inverted through an equation (see num_spots_inverted)
Median_inverted - Median coverage inverted (see above).
Area_inverted_mean - Average area of detected objects inverted. Ranges from 1.0 to 40,000 as Area_mean.
Area_inverted_std - Area inverted standard deviation.
X_inverted_mean - ???
X_inverted_std - ???
Y_inverted_mean - ???
Y_inverted_std - ???
Perim._inverted_mean - Mean of perimeter inverted.
Perim._inverted_std - Standard deviation of perimeter inverted.
BX_inverted_mean - Inverted BX - value
BX_inverted_std - ?? I cannot determine what BX_inverted is if I don't know what BX means.
BY_inverted_mean - See above.
BY_inverted_std - See above.
Width_inverted_mean - Inverted width values. Could be y = x because the graph . 1.667 to 34.
Width_inverted_std - Standard deviation values of widths.
Height_inverted_mean - Mean of inverted height-of-spots values.
Height_inverted_std - Standard deviation within the set of inverted height-of-spots values.
Major_inverted_mean - Inverted values of "major". Meaning of "Major_mean" is unkown, therefore, Major_inverted_mean cannot be fully realized.
Major_inverted_std - See above.
Minor_inverted_mean - See above
Minor_inverted_std - See above.
Angle_inverted_mean - See above.
Angle_inverted_std - See above.
Circ._inverted_mean - Mean of inverted circumference (of spots?) values
Circ._inverted_std - Standard deviation of inverted circumference (of spots?) values
Feret_inverted_mean - The inverted values of the mean of the feret diameter (distance between two parallel lines tangent to its boundary)
Feret_inverted_std - The inverted values of the standard deviation of the feret diameter (distance between two parallel lines tangent to its boundary)
IntDen_inverted_mean - Average integrated density
IntDen_inverted_std - Standard deviation of integrated density.
%Area_inverted_mean - Cannot be determined.
%Area_inverted_std - Cannot be determined.
RawIntDen_inverted_mean - The mean of the inverted raw integrated density values in the imamge.
RawIntDen_inverted_std - The standard deviation of the raw integrated density values in the image.
FeretX_inverted_mean - Mean of inverted feret x-coordinates.
FeretX_inverted_std - Standard deviation of of inverted feret x-coordinates.
FeretY_inverted_mean - Mean of inverted feret y-coordinates.
FeretY_inverted_std - Standard deviation of inverted feret y-coordinates.
FeretAngle_inverted_mean - Cannot be fully determined as I do not know what FeretAngle is.
FeretAngle_inverted_std - See above.
MinFeret_inverted_mean - Mean of the inverted values of the minimum feret diameters in the image.
MinFeret_inverted_std - Standard deviation of the inverted values of feret diameters in the image.
AR_inverted_mean - Mean of inverted aspect ratio values.
AR_inverted_std - Standard dev. of inverted aspect ratio values.
Round_inverted_mean - Mean of inverted roundness values.
Round_inverted_std - Standard deviation of inverted roundness values.
Solidity_inverted_mean - Mean of inverted solidity values.
Solidity_inverted_std - Standard deviation of inverted solidity values.
full_path - The full path to the file
classifier_pred_class - Manually classified through a classifier. How the classifier works is unkown.