Alignment Tab

The Alignment tab has features that deal with stitching images, moving layers and aligning one layer to another.


The following tools are available in the Alignment tab:

See Stitching

Select Stitch


Selects the node where four tiles have been stitched together.

For more information, see: Stitching

Stitch Manager


Opens the Stitch Manager window.

For more information on stitching and manual edits, see: Stitching

Regenerate Multiscale


The multiscale is a set of images that depict a layer when zoomed out. This makes zooming and scrolling operations faster than if all individual tiles were displayed.

The multiscale needs to be regenerated if captured tiles are modified to update the zoomed out view.



This tool moves the selected layer by clicking and dragging it.

View Anchors


Opens the Anchor Groups window. Here all the anchor groups that have been created throughout the project are displayed.


Once highlighted the anchors for that group are displayed in the overlay window.


When the user selects M1 lines, the anchors for that group are displayed in the overlay window. It says only “M1 lines” instead of M1 lines - M2 lines because it is an orthogonal alignment.


To add an anchor press the + button and a window will pop up like this:


The user then has to decide whether they want an interlayer alignment, a layer orthogonal tool, or a cell alignment (these are talked about in aligning layers).

In the ‘Anchor Group Settings’, the user can specify if ‘Align Anchors’ should be performed after each ‘Add Anchor’. This option should usually be turned on, but you can turn it off if the ‘Align Anchors’ process is taking too long.


For more information on anchors, anchor groups and layer orthogonality, see: Aligning Layers

Add Anchor


Adds a set of anchor points for the active anchor group.


Anchors are key in aligning two layers to one another


Select Anchor


Click and drag a box over any unwanted anchors. The anchors selected will now be highlighted in red.

Delete Anchors


Click to delete any highlighted anchors. Only anchors that have been selected using the Select Anchor tool are affected.

Align Anchors


If a bad anchor or group of anchors was removed the layer undergoing alignment will still be warped incorrectly. Clicking align anchors will snap back to fit the unaltered anchor points.

Alignment Review


Alignment Review opens a window that has many tools that assist in aligning one layer to another.


Set Review Boundary: Using the Select Area tool to set a boundary of review points for making the anchor grid.

Move to current: Moves the overlay window to center on the current alignment review point.

Accept: if the alignment does not need adjustment Accept will add an anchor at the review point.

Next: Move to the next review point.

Previous: Returns to the previous review point.

Calculate Bend Percentages: Under the Anchor Performance column a value is calculated for each anchor placed. The higher this value
the more warping the anchor caused.
Advance on New Anchor: Clicking this box will turn this feature on. Every time an anchor is placed or accepted the overlay will snap to the next
location an anchor should be placed for alignment consistency.

Straightening Guide


Displays a horizontal and vertical line that can be dragged around the screen. This tool is used to help verify the orthogonality of each layer.

Polygon Alignment

Polygon alignment is controlled by the Polygon Alignment window in the “Alignment” tab.


This tool is used for any case that a polygon and a reference layer that were already aligned get moved, or to tell Pix2Net that the layers are aligned. Here’s what the polygon alignment window looks like:


The button that looks like a pencil will tell Pix2Net to set a reference layer to a polygon layer of the user’s choice. If the user tries to set the reference layer of the “contacts” layer to “poly”, you will see a dialog like this:


This dialog shows up because the warp grid of the “polygon layer” differs from the warp grid of the “image layer”, and Pix2Net wants you to confirm that it is okay to synchronize the two warp grids. This should really only be an issue for existing projects. For future projects, the reference layer will be set when the polygon layer is created, so the user won’t see a dialog like this. Marking the polygon as ‘aligned’ means that the user is saying “yes, the reference layer is aligned to the polygon layer.” Now, let’s say that the user wants to use the feature that used to be called “Warp Polygons to Image”. If you move the image layer, then the next time you bring this window up, you will see “No” under the “Aligned” column. For example, here’s what it looks like after I move the “m2 lines” image layer:


When you click the align polygons to reference layer button, it will align the polygons back to the reference layer. The aligned portion will then say “yes” and the two layers will be aligned how they were before.