3. Main Settings

1. Main Settings Tab

1. Click the Add/View Paths button to pull up the data path window

   

   

   1. The Data Path is the full path to the folder containing the data files that will be processed
   2. + Add Path for additional paths, - Remove Path to delete paths
   3. Browse for or type path(s) into box(es)
   4. Find/View SubDirs to automatically find all the subfolders of the master folder you have imputed
      1. Check the subfolders you wish to use
      2. You can input a pattern in the top right corner and click the button to automatically check any subpath that contains that pattern
      3. Click submit to save your subpaths.
   5. Use the Pattern box to only display subfolders with a specific pattern
   6. Set Max Depth to how many folders past the master folder you wish to search past the master folder. I.E. folders in your master folder would be depth 1.
   7. Include Master will allow you to use the master folder as a data path. If you only want to use subfolders then make sure this is unchecked.
   8. Click Submit to save paths

2. Check Real-time Processing if needed. Real-time processing can be used to monitor folders for incoming data and have it processed in real-time. If data is already existing then leave this unchecked.

3. Channel Patterns will appear automatically once data paths are set in Step 2A

   1. Check patterns that need to be processed
   2. Custom Patterns can be checked and used in place of the automatically generated patterns. These custom patterns should be separated by commas, EX. CamA,CamB,CamC would mean CamA CamB CamC are the 3 patterns to be found for processing.
   3. Note that checking Custom Patterns will mean the auto-generated Channel Patterns will not be used

4. Set Step Size (stage scan interval) and check Objective Scan (if your data is already deskewed) if needed

5. The bottom boxes (pictured below) will decide what image processing will be done to the data.

   

   1. The leftmost box for each option that you want to be performed on the data. NOTE: selecting Decon Only will mean the data will only be Deconvoluted and nothing else (Deskew, Rotate, etc.) will run.
   2. Decon Column
      1. This column will cause a deconvolution to be performed after the selected option. Ex. Deskew with the Decon box checked will Deskew the data and then decon the Deskewed data.
   3. Overwrite Column
      1. This column will cause current results to be overwritten if there are any
   4. Save 16-bit Column
      1. This column will cause the results to be saved as 16 bit
   5. Only First TP Column
      1. Only compute first timepoint *(Only works for stitching now)

2. Main Advanced Settings

1. Skew Angle is the skew angle of the stage
2. XY Pixel Size is the pixel size in the xy dimensions
3. Reverse will invert the direction of the z-axis
4. sCMOS Cam Flip (unused)
5. You can set a Resampling by picking a type and setting a type and scale values in each axis
6. Input is Zarr is used when your input is Zarr files
7. Save as Zarr will save your output as Zarr files (if supported)
8. Save as 3D Stack will save each output as one 3D stack

3. Click the Next button on the main page and you will be taken to one of the next main Tabs according to your selections