#Save svg files for registration if CASE == 0: for sliceNum in slices: filenameAtlas = '/mnt/jarahubdata/atlas/AllenCCF_25/JPEG/allenCCF_Z{}.jpg'.format( ccfSlice[sliceNum]) filenameSlice = os.path.join(HISTOLOGY_DIR, subject, jpgFolder, '{}tl.jpg'.format(sliceNum)) filenameSVG = os.path.join(HISTOLOGY_DIR, subject, registrationFolder, '{}_pre.svg'.format(sliceNum)) (atlasSize, sliceSize) = ha.save_svg_for_registration(filenameSVG, filenameAtlas, filenameSlice) #Read coords, apply transform, output counts per area elif CASE == 1: annotationVolume = ha.AllenAnnotation() allSliceCounts = [] for sliceNum in slices: filenameSVGPost = '/mnt/jarahubdata/jarashare/histology/{}/{}/{}.svg'.format( subject, registrationFolder, sliceNum) (scale, translate, affine) = ha.get_svg_transform(filenameSVGPost, sliceSize=[1388, 1040]) filenameCSV = '/mnt/jarahubdata/jarashare/histology/{}/{}/{}.csv'.format( subject, registrationFolder, sliceNum) coords = ha.get_coords_from_fiji_csv(filenameCSV, pixelSize=4.0048) newCoords = ha.apply_svg_transform(scale, translate, affine, coords) structIDs = annotationVolume.get_structure_id_many_xy( newCoords, ccfSlice[sliceNum]) structNames = [ annotationVolume.get_structure_from_id(structID)
import os import matplotlib.image as mpimg import numpy as np from matplotlib import pyplot as plt from jaratoolbox import histologyanalysis as ha reload(ha) an = ha.AllenAnnotation() imageDir5xMerge = '/home/nick/Desktop/mergedImages_anat036_5x_thal' subject = 'anat036' slices = ['p1d1', 'p1d2', 'p1d3'] ccfSlice = {'p1b6':163, 'p1c1':167, 'p1c2':171, 'p1c3':175, 'p1c4':179, 'p1c5':183, 'p1c6':187, 'p1d1':191, 'p1d2':195, 'p1d3':199, 'p1d4':203, 'p1d5':207, 'p1d6':211, 'p2a1':215, 'p2a2':219, 'p2a3':223, 'p2a4':226, 'p2a5':229,