LMD Export

This feature is not enabled by default. To enable, open the options and type LMD in the search bar. Check the box to enable LMD export then apply the change.

To open the export window go to File->Export->Outlines to XML for LMD. If this option is grayed out, then your current image does not have any outlines present in it. Outline features (outlines, nuclear membrane outline, cell membrane outline, or vesicle outline) must be present on the open image for the option to not be grayed out.

Root Set: This is the top level of all the object sets in the Hierarchy. In the example below, Meshes is the only Root object set in the hierarchy. It is possible to have multiple root object sets.

Parent Set: This a broad term for the top level of any set that has child sets below it. Using the same example, there are multiple “Parent sets” as well as the root (“Meshes”) which is also a parent in this case. This will be a common theme of sets being multiple “types”.

Child Set: Another broad term for sets that are under a parent level in the hierarchy and displayed as indented. Parents can be children, and children can be parents depending on the relationship to downstream subsets.

There are 2 modes to LMD Export. The first time you open the window, you will be in the default mode that does not support capID. To switch to capID mode, click the check-box “Enable CapID Export”.

This mode operates on a root level object set. It expects the highest-level object set to have outlines. Even if its children have outlines, if the root level object set does not have outlines, then nothing will get exported. This is used for very basic operations without a well plate, or for exporting all outlined feature cut out into one place.

This mode is for advanced exporting/dissection, as well as for users who plan to use a well plate/test tubes/petri dishes/etc or have a complex object set hierarchy. This will also include the location (CapID in the well plate) where each object will go. This mode supports non well plates as well. It can be setup to support test tubes, dishes, or any other collection vessels.

Shared properties:

For Non-Cap ID, this will cover everything you need. For cap ID export, see the capID export section below for more information.

Calibration:

From the top the “select calibration” is a requirement for the LMD system to align itself and it must have a value in order to export. If you haven’t created a calibration yet, you can click on the create calibration and add 3 point annotation. The value will be shown in the window.

Skipping the middle part for now, jump to the bottom and look at the slider options

Dilate Outlines Factor:

This feature allows you to expand the outline a little bit, so when you are cutting, you give the object a little space.

Example:

Here’s a simple showing of how dilation works with a simple demo shape outline given a 5 factor dilation. The drawn results are shown below. As you can see dilating makes pointed edges more round and can add more points to the image, lowering the possibility of cutting into the cell and losing some parts of it

Object Outline Complexity Reduction Factor:

Object Outline Complexity - describes how many points are in an outline. The Reduction Factor is how to simplify (reduce points in) that shape. It’s difficult to determine how complex a shape is just by looking at the outline as demonstrated in an example below:

Given these simple shapes, you might assume that the triangle, square and octagon consists of 3,4, and 8 points. In reality the triangle is 128 points, square is 160, and octagon is 288. There may not be any benefit to visit each point individually and will result in increased time.

Here is an example of the effect of adding Reduction Factor. With the default value of 6, now our shapes are more realistic to what you would expect and less spots for the LMD laser to have to address.

With the Reduction Factor of 6, there is no discernible difference in the shape in this example although the cutting process will be sped up.

Bypass Reduction for shapes small than:

Due to the nature of complexity. Reduction for shapes with not too many points may not be simplified or they might end up as just a straight line, just a point, or they might cut corners through the object you’re trying to cut. Due to this, Bypass Reduction parameter allows you to skip complexity reduction on shapes that aren’t as “complex” as it is often difficult to know how many point actually exist in the outline just by looking at it.

All you need to do is select the object set you want to export and make sure the export parameters are set to your preference https://aivia-software.atlassian.net/wiki/spaces/AW/pages/2575400961/LMD+Export#Shared-properties%3A ) then click the export button in the bottom right.

If you cannot find your object set in the drop-down menu, then your object set is not a root set (https://aivia-software.atlassian.net/wiki/spaces/AW/pages/2575400961/LMD+Export#Hierarchical-Definitions%3A ) and will need to use CapID export which can accomplish the same thing as non-capID export

This is a powerful mode that enables you to export object sets in many different ways.

By default, you can click to add the selected object set to the well plate if you want to manually add it (automated options are available - see well ordering below). The selected object set must have outlines in it. If it does not, it will error out and let you know. Even if it had a child with the outlines, it will not let you add it, you must select the object set that actually has the outline in order for the set to be added to the well plate.

“Multi-plate” - This feature gives you access to multi-plate export. When you use an automated well populating option if you have more samples than fit on the first well plate you will get a prompt, if you click yes multi-plate mode will activate. Each of these plates are interactable and modifiable. So you can change the plates if you want to. Adding plates on their own not supported at the moment, automated plate filling required to make additional plates . On export you will get a file for each plate exported. The format is filename_plate#.xml.

“Select Object Set” - gives you access to the entire hierarchy of object sets. NOTE: the color to the left of the name will correspond with location on the virtual well plate.

“Collector Selection” - This enables you to change the layout of the visual well plate in the window. There are 4 preset options (96, 384, 1536 well plates, and PCR Caps) as well as 5th custom option. The 5th custom option will let you set the well plate rows and columns to whatever you need it to be (Max 36 x 48). NOTE: Changing the well plate will clear any set wells on it currently.

“PCR Caps” - this option is specifically for single line export. There are no numbers associated with this option (only letters). Only columns can be adjusted (max 48 (AU))

“Samples per Well” - Determines how many objects will go into each well. One caveat to this is if you already have a well ordering in place, you need to redo the well ordering to get correct logic with samples per well applied to it.

“Add unused row/col to well plate” - This will gray out and remove objects starting with the outer rows/columns of the well plate and will work inward as you add more. Great option if your well plate is too large to fit into the device or if you have a case where your outer wells are not needed. Upon hovering over a well the tool tip, you can see which well is disabled/enabled. You will not be able to interact with disabled wells.

“Well Ordering” - There are 4 choices here (including the clear button) these are all automated buttons that will fill the well plate according to specific hierarchical rules explained below. These rules will be using the hierarchical definitions https://aivia-software.atlassian.net/wiki/spaces/AW/pages/2575400961/LMD+Export#Hierarchical-Definitions%3A . All of these options evaluate whether the object set has outlines or not, if the object set does not have outlines, it will be excluded in all these options.

“One Set per Row” - This option works on the immediate child level of the selected parent (if no children are present it will default to itself). The sets that are added will be the children (it only goes 1 step down) of the selected parent object set. For each child of the selected parent, 1 row will be set to the color of that object set until you run out of rows or child object sets. If the object set does not have children, then it will just add itself as long as it has outlines in its object set. This option supports smart filling where if there are not enough outlines in an object set to fill a row, then it will fill accordingly based on the number of samples.

“Evenly Distribute” - This option works on the immediate child level of the selected parent (if no children are present, it will default to fill all behavior). The sets that are added will be the children (it only goes 1 step down) of the selected parent object set. For each child of the selected parent, the well plate will be evenly distributed between all of them.

“Fill All” - This option works on the selected object set only (not children). If your selected object set does not contain an outline, it will error out, even if it contains a child set with outlines. You must select the object set that has the outlines for this option. This option supports smart filling where it will only fill the well plate to the number of outlines in the object set and factors in the number of samples in the calculation.

After assigning to well plate check the bottom next to the export button if you see this yellow text then you have overlap of outlines and neither will be exported Using automated assignment should prevent this from happening. If automated assignment doesn’t work for you, then try not to overlap a parent set with a child set, this leads to duplicate outlines when results in removal of them.

“Clear all” - removes everything from the well plate, removes all multi-plates, and resets added unused row/column to 0.