runInitializeElastix(parameter) pts = runCellCoordinateTransformation(parameter) io.writePoints(os.path.join(basedirectory, 'cells_to_autofluo.csv'), pts) ## Visualize cfos to auto points parameter.ImageProcessing.CellCoordinateFile = pts parameter.ImageProcessing.CellTransformedCoordinateFile = None pts2 = runCellCoordinateResampling(parameter) ds = dataSize(os.path.join(basedirectory, 'autofluo_for_cfos_resample.tif')) voximg = vox.voxelizePixel(pts2, ds) io.writeDataStack( os.path.join(basedirectory, 'points_transformed_cfos_to_auto.tif'), voximg) #pts0 = io.readPoints(os.path.join(basedirectory, 'cells.csv')); ############################################################################## # Transform Points matched to Autofluorescence to Atlas Reference ############################################################################## import os from iDISCO.Parameter import * from iDISCO.Run import runInitializeElastix, runCellCoordinateTransformationToReference import iDISCO.Visualization.Plot as Plot
#Processes to use for Resampling parameter.Resampling.Processes = 4; resampledImage = runResampling(parameter); print("Resampled image saved as %s" % resampledImage) # voxelize result voximg = vox.voxelizePixel(acenters, referencedata.shape); io.writeDataStack(os.path.join(basedirectory, 'Synthetic/points_transformed_pixel.tif'), 5000* voximg) if verbose: transformdata = io.readData(os.path.join(transformdir, 'result.mhd')); referencedata = io.readData(os.path.join(basedirectory, 'Synthetic/test_iDISCO_resample.tif')) Plot.plotOverlayPoints(transformdata * 0.01, acenters); Plot.plotOverlayPoints(referencedata * 0.01, acenters);