The recipe file

BakingTray uses so-called "recipe" YML files to determine the settings with which an acquisition is conducted. A recipe contain settings that are deemed more or less likely to change between samples:

• sample.ID - A string defining the name of this sample. This is used to create directory names and so can not include problematic characters. If these are entered they are automatically substituted with something better.

• sample.objectiveName - The name of the objective. This can be any string and is not used for anything.

• mosaic.sectionStartNum - Number defining the index of the first section. Generally, this should be left at 1

• mosaic.numSections - Integer defining how many sections to take

• mosaic.cuttingSpeed - How fast to cut the block in mm/s

• mosaic.cutSize - How long the cut should be in mm

• mosaic.sliceThickness - How thick the cut slice should be in mm

• mosaic.numOpticalPlanes - Integer defining into how many optical planes the slice should be divided. e.g. if the slice thickness is 0.1 (100 microns) and the number of optical planes is 10 then BakingTray will image 10 sections spaced 10 microns apart.

• mosaic.overlapProportion - The proportional overlap between adjacent tiles in x/y. A value of "0.05" means 5% overlap. We don't use the overlap to guide tile placement, so this number doesn't have to be large.

• mosaic.sampleSize.[XY] - The size of the sample in mm along X and Y.

• mosaic.scanmode - Currently this should be the string tile. If other scan modes are added later, such as stage-scannng, or auto-finding the sample then this will be changed.

Generally you will edit the recipe via the GUI.