Go to the field of view (FOV) of interest, right-click, and select RACT - ART in the menu. This will open Raster Annotation Correction Tool (RACT) page.
Disable "Brush Auto-Fill".
Select a class in "Regions".
Select a "Brush Size" (e.g., 10).
Outline your areas (Shift + Left Mouse Key allows you to draw a new object).
New pop-up "Start a new session" will appear, and you need to confirm the raster annotation set name. The vector annotation set name is pre-filled here, but can be modified.
Always wait until the saving is completed (Wait until the "Saved" message appears in the top panel).
Ensure the area outlines are closed before using the fill tool to color all pixels within the area with the correct class (left-click).
Finish session Ctrl + S to save your latest changes and start a new session on the next prompt.
Hints
Ctrl + S to save the latest changes during annotation and Finish session.
Disable Brush Auto-Fill to delete/manipulate region areas within a region.
Right mouse click allows you to remove the class pixels (works with both brush and the Reclassify (aka Fill) tool).
Shift + Left Mouse Key allows you to draw a new object.
Hold ALT key to pan & zoom in the image.
TAB key allows you to switch between the current and previous brush size.
Create a raster annotation set (SSTC)
Go to the field of view (FOV) of interest, right-click, and select RACT - SSTC in the menu. This will open Raster Annotation Correction Tool (RACT) page.
Load proposed annotations.
Apply Recalculate.
If annotation errors are detected, Confirm error.
Manually correct the errors in the annotations.
New pop-up "Start a new session" will appear, and you need to confirm the raster annotation set name. The vector annotation set name is pre-filled here, but can be modified.
Repeat step 3 until annotations are correct.
Finish session (Ctrl + S) to save your latest changes and start a new session on the next prompt.
Hide all layers.
Show region layer (toggle visibility ON).
Correct region outlines as needed with left-click.
"Start a new session" will appear, you need to confirm the annotation name to save the changes under the same raster annotation set.
(Optional) Apply Recalculate.
Show cell center layer.
Toggle Recenter ON only if you want to enable repositioning of the cell centers during Recalculate.
Place missing cell centers (left-click) or remove cell centers (right-click).
Show all layers.
Apply Recalculate.
If annotation errors are detected, Confirm error.
Manually correct the errors in the annotations.
Repeat step 17 until annotations are correct.
Correct other annotation types (i.e., cell membranes, nuclei membranes, exclusions) as needed.
Finish session Ctrl + S to save your latest changes and start a new session on the next prompt.
Hints
Ctrl + S to save the latest changes during annotation and Finish session.
Disable Brush Auto-fill to delete/manipulate region areas within a region.
If you decide to enable/disable Recenter after Recalculate is complete, edit the position of a single center point to reset the review state, and re-run Recalculate.
Shift + Left Mouse Key allows you to draw new cells and nuclei.
Hold ALT key to pan & zoom in the image.
TAB key allows you to switch between the current and previous brush size.
