Reading Back-up Text Files to TIFFs

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import numpy as np
import pandas as pd
import palmettobug as pbug

C:\Users\caiello\AppData\Local\miniconda3\envs\Palmettobug3.10\lib\site-packages\tqdm\auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from .autonotebook import tqdm as notebook_tqdm

CHANGE This DIRECTORY to match a valid directory on your computer if you testing this tutorial on your own machine!

Also NOTE!! – This example notebook does not operate on any bundled example data . Instead, you must supply your own folder of .txt files from the Hyperion imaging system and your panel files:

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my_computer_path =  "C:/Users/Default/Desktop"

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txt_file_dir = f"{my_computer_path}/tour_text_files_here"    ## should contain a set of .txt files exported by SBI's Hyperion imaging system
to_dir = f"{my_computer_path}/write_images_to"
panel_dir =  f"{my_computer_path}/your_panel_file_here/panel.csv"
panel = pd.read_csv(panel_dir)

pbug.txt_folder_to_tiff_folder(txt_file_dir, to_dir, hpf = 50, ome_tiff_metadata = True, resolutions = [1.0,1.0], panel = panel)

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