Use Curation Module

1. Data preparation

Organize your image data into directories as the following:

  • Raw image directory

    • Contains your original microscopy image data

    • Accepts: .tiff, .ome-tiff, .czi

  • Segmentation 1 directory

    • Contains your segmentation of the structure of interest

    • Accepts: .tiff, .ome-tiff, .czi

  • Segmentation 2 directory (optional)

    • Contains optional complementary segmentation image data, which could be generated from the same raw image data for the same structure but using different segmentation algorithms.

    • It is useful when Seg 1 fails predictably in certain cases (e.g. a segmentation that works during mitosis to supplement an interphase segmentation)

    • Accepts: .tiff, .ome-tiff, .czi

Other requirements

  • At least 4 raw images and 4 corresponding segmentation files are required. Using a larger number of images is strongly recommended to train a robust and accurate segmentation model.

  • The number of files should be consistent across directories

  • It’s important to have your raw & segmentations named appropriately for the plugin to display them correctly. For example:

    • AICS-13_1516_raw.tiff (raw)

    • AICS-13_1516_segmentation_interphase.tiff (seg 1)

    • AICS-13_1516_segmentation_mitotic.tiff (seg 2)


2. Select input data

After applying the “Start a new model” option with an appropriate model name, the plugin will display the Curation tab as shown below:

screen 1 of curation tab of Segmenter ML plugin in *napari*

STEPS

  1. Directory – select the directories you have prepared

  2. Image channel – the image channel dropdown will display available channels detected in the directories you have loaded. Channel often starts at 0

  3. Click Start


3. Start curation

VIEWPORT

images layer in Layer List panel

In the viewport, your images will be displayed one set at a time, with the segmentations overlaid on top of the raw image in the following order top to bottom:

  • Seg 2 (if available): label layer: teal color

  • Seg 1: label layer: orange color

  • Raw: image layer: grayscale color

PLUGIN INTERFACE

screen 2 of curation tab

a. Sorting

  • Revisit the concept of sorting if needed

STEPS

sorting interface
  1. User this image for training?

    • Select Yes (the default selection) to use the image pair for training

    • Select No to skip this image pair

  2. Select a base segmentation

    • Seg 1 is selected by default

    • if Seg 2 is available, you can choose to use either Seg 1 or Seg 2

  3. Click Next to proceed to the next image pair if no further action needed (e.g., excluding or merging),

    • The progress bar displays your current progress, and show how many image pairs you have reviewed

      Curation progress section
    • When at least 4 image pairs have been selected to use for training, the Save curation progress button will be enabled for you to save your progress

      Save curation progress

b. Create an excluding mask (OPTIONAL)

STEPS

1. Click the Create button under the Excluding mask section

create an excluding mask

2. Your cursor automatically changes to the polygon drawing tool (cross-hair icon over the viewport)

3. Start drawing shapes to cover areas of the image you want to exclude, double-click to close the shape, and review in z using the slider at the bottom of the viewport to ensure the shapes are still appropriate

draw excluding mask
slider to navigate through z slices

Tip

Precision isn’t critical when drawing, as long as the subpar segmentation areas are adequately covered. We aim to make this process quick, especially since there may be a large number of images for you to review.

4. When you’re finished with all shapes, click Save to save your excluding mask

5. Alternatively, if you:

  • no longer need an excluding mask, click Delete

  • wish to start over, click Delete then click Create to add a new excluding mask

Note

Each image pair will have only one excluding mask, clicking Save multiple times will resave the same mask or clicking Create multiple times will overwrite the previously created mask


c. Create a merging mask (OPTIONAL)

  • Revisit the concept of merging if needed

  • This function is only enabled if Seg 2 is also present in additional to Seg 1

STEPS (similar to the Excluding mask’s steps)

1. Click the Create button under the Merging mask section

create merging mask

2. Your cursor automatically changes to the polygon drawing tool

3. Start drawing shapes to cover areas of the image you want to be overwritten, double-click to close the shape, and review in z using the slider at the bottom of the viewport to ensure the shapes are still appropriate

draw merging mask
slider to navigate through z slices

4. When you’re finished with all shapes, click Save to save your merging mask

5. Alternatively, if you:

  • no longer need a merging mask, click Delete

  • wish to start over, click Delete then click Create to add a new merging mask

Note

Each image pair will have only one merging mask, clicking Save multiple times will resave the same mask or clicking Create multiple times will overwrite the previously created mask

Warning

Merging mask and excluding mask can’t overlap each other.


4. Complete curation

Upon reaching the last image indicated in the progress bar

  • Click Finish next to the progress bar

click finish to complete curation
  • Your curation progress will be saved automatically

  • A dialog will prompt you to switch to the Training tab to start training

curation complete dialog box

Caution

  • If you close the plugin while in the middle of the curation process, the plugin will not save your progress.

  • Your curation progress will only be saved once you have finished curating your dataset or have clicked Save curation progress.

  • Curation progress is saved to a CSV and can be used for training immediately once saved, but currently it cannot be used to resume curation if you exit the curation process.