beatrizserrano / test_multipage Goto Github PK

1. The output features of the ExampleHuman dataset is in the folder results_separate_images.

2. Python script to create a multi-page tiff from numpy objects (by @davelopez).

• Input: original ExampleHuman tiff files to use them as numpy objects
• Output: multi-page tif
• Dependencies: imageio

Part of this code can be included in the IDR download tool to save multiple numpy objects (from getTile) into one file instead of saving separate tif files.

NOTE: All the files within a multi-page file need to have the same dimensions. The batches of images should never combine images from different datasets (they are cropped differently).

3. To run CellProfiler using the multi-page tif some adjustments are needed:

• Module Metadata
  • Metadata extraction method -> Extract from image file headers
• Module NamesAndTypes (this config might not be needed)
  • Assign a name to -> Images matching rules
  • Match All of the following rules
  • Select the rule criteria:
    • Metadata - does - Have Frame matching - 0
    • Image - Is - Stack frame

The output features are in the folder results_multipage_tiff.