SegmentationBiomarkerCTC/datasets_gedi_419_2.ini at main · amatov/SegmentationBiomarkerCTC · GitHub

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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
; Global parameters

; The directory relative to which the directory with the original images (datadir) is specified
databasedir = /home/mihaylov/Dropbox/cornell/Dropbox/Alex/CTC/Gedi

; The directory relative to which the manual coordinates file (coordinates) is specified
xlsbasedir = .

; The direcotry relative to which the result directory (resdir) is specified
resbasedir = /home/mihaylov/public_html/jedi/gedi_419_tiles_512x512_1

; The directory where to cache the segmented images
segdir = /home/mihaylov/tmp/ctc_seg

; The pictures used as labels for images 512 pixels wide
labelCK_512 = label_CK.png
labelDAPI_512 = label_DAPI.png
labelCD45_512 = label_CD45.png

; The pictures used as labels for images 1024 pixels wide
labelCK_1024 = label_CK_1024.png
labelDAPI_1024 = label_DAPI_1024.png
labelCD45_1024 = label_CD45_1024.png


[gedi_419_z1]
datadir = 419 with coordinates/ChipA0419_fullregion
coordinates = ManCoords_GEDI_419_z1.xls
nameCK = ChipA0419_fullregion_z1c1_ORG.tif
nameDAPI = ChipA0419_fullregion_z1c3_ORG.tif
nameCD45 = ChipA0419_fullregion_z1c5_ORG.tif
positions = 1
num_tiles_x = 42
num_tiles_y = 14
maxDist = 9
rectSize = 31
minCK = 0
maxCK = 4000
minDAPI = 0
maxDAPI = 8000
minCD45 = 0
maxCD45 = 3000
coeffCD45 = 1.1
maxCD45pixels = 3


[gedi_419_z2]
datadir = 419 with coordinates/ChipA0419_fullregion
coordinates = ManCoords_GEDI_419_z2.xls
nameCK = ChipA0419_fullregion_z2c1_ORG.tif
nameDAPI = ChipA0419_fullregion_z2c3_ORG.tif
nameCD45 = ChipA0419_fullregion_z2c5_ORG.tif
positions = 1
num_tiles_x = 42
num_tiles_y = 14
maxDist = 9
rectSize = 31
minCK = 0
maxCK = 4000
minDAPI = 0
maxDAPI = 8000
minCD45 = 0
maxCD45 = 3000
coeffCD45 = 1.1
maxCD45pixels = 3


[gedi_419_z3]
datadir = 419 with coordinates/ChipA0419_fullregion
coordinates = ManCoords_GEDI_419_z3.xls
nameCK = ChipA0419_fullregion_z3c1_ORG.tif
nameDAPI = ChipA0419_fullregion_z3c3_ORG.tif
nameCD45 = ChipA0419_fullregion_z3c5_ORG.tif
positions = 1
num_tiles_x = 42
num_tiles_y = 14
maxDist = 9
rectSize = 31
minCK = 0
maxCK = 4000
minDAPI = 0
maxDAPI = 8000
minCD45 = 0
maxCD45 = 3000
coeffCD45 = 1.1
maxCD45pixels = 3