io¶

pysmFISH.io.nd2_to_npy(gene, raw_data_gene_fname, tmp_gene_dir, processing_hyb, use_ram=True, max_ram=150000000000)[source]¶

Function used to convert Nikon ND2 files in numpy arrays. Important: require the nd2reader (https://github.com/jimrybarski/nd2reader) pip install “nd2reader==2.1.3”. There is a new version based on pims but need to be tested The input ND2 file will have only one channel and will be converted in a binary npy.

gene: str: Name of the gene to process (ex. Aldoc)
raw_data_gene_fname: str: Path to the ND2 file (ex. ‘/Users/simone/Desktop/test/ND2conversion/BW_Aldoc.nd2’)
tmp_gene_dir: str: path to the folder where to save the npy files
processing_hyb: str: Name of the processing_hyb to process (ex. EXP-17-BP3597_hyb2)
use_ram: bool: If True the images are written first in ram until max_ram is reached
max_ram: int: Size of the RAM that can be used as temporary storage