General Information for deepflash2

When a star (*) appears in the name of a button a change in the data or selection was recognized by the program. When you press the according button the change will be applied.

Supported image formats

We recommend ImageJ/Fiji to format your Images. Click to install Fiji/ImageJ.

DeepFlash2 can handle different types of imagedata. Recommended image formats are jpeg , png, or tiff.

You should avoid gif image format.

Required Folder Structure and Naming Convention to access you data

Required Folder Structure and Naming Convention when using google drive:

Note: You have to follow this section when using google drive as a storage for the data you want to use with deepFlash2. This applies to the local installation as well as

>to google colab.

Main directory

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GT Estimation

[folder] GT_estimation
  [folder] expert1
    [file] mask1.png
    [file] mask2.png
  [folder] expert2
    [file] mask1.png
    [file] mask2.png
  [folder] expert3
    [file] mask1.png
    [file] mask2.png

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Training

[folder] Training
  [folder] images
    [file] 0001.tif
    [file] 0002.tif
  [folder] masks
    [file] 0001_mask.png
    [file] 0002_mask.png

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Prediction

[folder] Prediction
  [folder] images
    [file] 0001.tif
    [file] 0002.tif
  [folder] ensemble
    [file] unext50_deepflash2_model-1.pth
    [file] unext50_deepflash2_model-2.pth