Coloring of segmentation images

[tischi]

@davodogster

The label mask class images that can be outputted now can be coloured running this IJ macro command:

run("glasbey_inverted");

Or in the Menu:

The applies the Glasbey LUT to the image which gives each gray value a different color.

In below example the background class has a label of 1, and the class for the blobs has a label of 2.

Shall I automatically apply this LUT to the segmentation images? I think it would be a good idea...

[davodogster]

Yes please I think it should automatically be applied and work for a single image or a folder of images.

---

From: tischi notifications@github.com Sent: Friday, June 21, 2019 5:35:51 PM To: embl-cba/fiji-plugin-cats Cc: Sam Davidson; Mention Subject: [embl-cba/fiji-plugin-cats] Coloring of segmentation images (#21)

@davodogsterhttps://github.com/davodogster

The label mask class images that can be outputted now can be coloured running this IJ macro command:

run("glasbey_inverted");

Or in the Menu:

[image]https://user-images.githubusercontent.com/2157566/59900000-1335aa00-93f7-11e9-8a9b-574e97c82c93.png

The applies the Glasbey LUT to the image which gives each gray value a different color.

In below example the background class has a label of 1, and the class for the blobs has a label of 2.

[image]https://user-images.githubusercontent.com/2157566/59899948-dff31b00-93f6-11e9-9af9-cdb0f925d53e.png

Shall I automatically apply this LUT to the segmentation images? I think it would be a good idea...

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/embl-cba/fiji-plugin-cats/issues/21?email_source=notifications&email_token=AK7R4HDSOS3MU4Z2Y3FR33TP3RSDPA5CNFSM4H2LW3CKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4G24BLXQ, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AK7R4HBXEPZRRIODMBKAEFTP3RSDPANCNFSM4H2LW3CA.

[tischi]

Ok. I will do this.

[tischi]

TODO: Add class colouring to segmentation output.

[davodogster]

Hi Christian can you enable us to apply a classifier to a folder of images and save all of the classification outputs with class coloring multiple labels in one image.

[davodogster]

Also, I just used the advanced classification option (can only classify one image, not a directory), and I selected to output all probabilities in one image (binary classification). The result was a multiclass grayscale with many different values representing many different probabilities.