TIFF extractor manager module

class library.image_manipulation.tiff_extractor_manager.TiffExtractor

Bases: library.image_manipulation.parallel_manager.ParallelManager

Includes methods to extract tiff images from czi source files and generate png files for quick viewing of downsampled images in stack

create_web_friendly_image()

Create downsampled version of full size tiff images that can be viewed on the Django admin portal. These images are used for Quality Control.

extract_tiffs_from_czi()
This method will:

  1. Fetch the meta information of each slide and czi files from the database

  2. Extract the images from the czi file and store them as tiff format.

  3. Then updates the database with meta information about the sections in each slide

Parameters

  • animal – the prep id of the animal

  • channel – the channel of the stack image to process

  • compression – Compression used to store the tiff files default is LZW compression