batch_process

The processor set of scripts to batch process a group of samples. This can be used from the GUI, from the CLI or interactively from the python interpreter

class BatchProcessor(progress_watcher, results_folder=None, params=None)

Bases: object

process_folders()

batch_crop(folder, crop_x=0, crop_y=0, suffix='_cropped')

convert_to_cm_2_1(folder, atlas_base_name='ABA_25um')

main(samples_file)

patch_pipeline_name(configs, cells, vasc)

process_folders(folders, align=False, cells=False, vasc=False)

process_sample(configs, align=False, cells=False, vasc=False)

realign(folder, atlas_base_name='ABA_25um')

rescale_channel(folder, atlas_base_name=None, dest_resolution=(3, 3, 6), n_cpus=None, channel='raw', ext='.tif', chunk_size=1)

Used to rescale to create e.g. test samples that can be ran quickly

Parameters:

• str (atlas_base_name) – The experiment folder with the tiles

• str – The base name of the atlas that serves as a file prefix for the atlas files

• tuple (dest_resolution) – The desired resolution

Returns

rescale_img(f_path, scaling_factor)

voxelize_folders(folders, align=False, cells=True, vasc=False)

voxelize_sample(configs, align=False, cells=False, vasc=False)