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9. Useful Tools Settings

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Matthew Mueller edited this page Jan 7, 2025 · 29 revisions

1. Crop

Crop

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  4. Crop Type can be fixed, moving, or center
  5. Parse Cluster will attempt to submit cluster jobs if a scheduler is available
  6. The crop’s 3D Bounding Box can be set by entering the desired values into the spinboxes
  7. CPUs Per Task sets the desired number of cores to use for a cluster job
  8. Use Master Compute Node will also use your current node to process cluster jobs if it is checked
  9. Job Log Dir will set the directory where you would like your job logs to output to (This can usually just be left as is)
  10. Start Coord of Last Timepoint is the start coordinates of the last timepoint (I.E. if your crop type is moving)
  11. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank
  12. Save as 16 Bit will output data as 16 bit if checked
  13. Input is Zarr should be checked if your input data is in the Zarr format
  14. Large Zarr should be checked if your input data is large scale Zarr data
    1. Only used if using zarr files
  15. Save as Zarr will save your output as Zarr files
  16. Block Size in Y, X, and Z are the block sizes of each axis
    1. Only used if using zarr files
  17. Batch Size in Y, X, and Z are the batch sizes of each axis
    1. Only used if using zarr files
  18. Add Padding will pad the region outside the bbox if it is checked

2. FFT Analysis

FFT Analysis

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  4. XY Pixel Size is the pixel size in the x and y axes in Microns
  5. Actual Pixel size in Z is the actual pixel size in the z axis
  6. Out Pixel Size is the pixel size for the output
    1. This value will apply to all axes
  7. Out Size in Y, X, and Z are the axis sizes of the output image
    1. These should all be the same size and not larger than the size of your smallest axis.
  8. Save 3D Stack will save the output as a 3D stack if checked
  9. Set Background as needed
  10. Interp Method is the interpolation method that will be used

3. FSC Analysis

FSC Analysis

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Channels should map to your channel patterns
  4. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  5. XY Pixel Size is the pixel size in the x and y axes in Microns
  6. Actual Pixel size in Z is the actual pixel size in the z-axis
  7. dr is the interval to get the resolution
  8. dtheta is the angle interval
  9. resThresh is the threshold that can be set from 0-1
  10. resThreshMethod can be fixed, half-bit, or one-bit
  11. resAxis is the axes that will be used for the averaging
  12. Half Size in Y, X, and Z are the axis sizes of the output image
    1. These should all be the same size and not larger than the size of your smallest axis.
  13. The 3D Input Bounding Box can be set by entering the desired values into the spinboxes
  14. Suffix will set the suffix of the output filename
  15. iterInterval is the interaction interval for the FSC resolution plot
  16. Master Compute will also use your current node to process cluster jobs if it is checked

4. Image List Generator

Image List Generator

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Generation Method is the method used to generate the Image List
    1. If your file names contain definable Tile Patterns (see 4.4), you can use tile_position
    2. If your file names are more custom and do not have definable Tile Patterns, you can use tile_list and manually define them
    3. Note: You must have information for all 5 dimension but you can leave dimensions as zero. (Ex: _ch0_0000t in all file names if you were only stitching in xyz)
  4. Tile Patterns are the patterns used to map the timepoints (T), channels (C), x-axis, y-axis, and z-axis
  5. DS should be set based on whether the data is deskewed (DS) or not
  6. DSR should be set based on whether the data is deskewed and rotated (DSR) or not
  7. XY Pixel Size is the pixel size in the x and y axes in Microns
  8. Actual Pixel Size in Z is the actual pixel size in the z-axis
  9. Skew Angle is the skew angle of the stage
  10. Axis Order is the tile indices axis order
    1. A negative sign can be used to indicate a reversed direction in an axis (I.E. -x,y,z means scan in a reversed direction in the x-axis)
  11. Data Order is the data axis order
  12. Zarr File should be checked if your input data is in the Zarr format
  13. Objective Scan should be checked if your data is already deskewed
  14. IO Scan is inverted objective scan. This should be checked if you are scanning in the DSR space
  15. Overlap Size is the size of the overlap in stage coordinates
  16. Overlap Size Type is the type used for Overlap Size
  17. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank

5. Imaris Converter

Imaris Converter

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  4. Pixel Sizes in Y, X, and Z are the pixel sizes of each axis
  5. Block Sizes in Y, X, and Z are the block sizes of each axis
    1. Only used if using zarr files
  6. The 3D BBox can be set by entering the desired values into the spinboxes
  7. zarrFile should be checked if your input data is in the Zarr format
  8. Parse Cluster will attempt to submit cluster jobs if a scheduler is available
  9. CPUs Per Task sets the desired number of cores to use for a cluster job
  10. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank
  11. Job Log Dir will set the directory where you would like your job logs to output to (This can usually just be left as is)

6. MIP Generator

MIP Generator

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  4. Axis will determine the axis from which to generate the MIP (If multiple are selected then the last axis will be used)
  5. Zarr File should be checked if your input data is in the Zarr format
  6. Large Zarr should be checked if your input data is large scale Zarr data
  7. Batch Size in Y, X, and Z are the batch sizes of each axis when using zarr files
  8. Parse Cluster will attempt to submit cluster jobs if a scheduler is available
  9. CPUs Per Task sets the desired number of cores to use for a cluster job
  10. Use Master Compute Node will also use your current node to process cluster jobs if it is checked
  11. Job Log Dir will set the directory where you would like your job logs to output to (This can usually just be left as is)
  12. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank
  13. Save as 16 Bit will output data as 16 bit if checked

7. OTF Masking

OTF Masking

  1. PSF Filename is the full path to the PSF file
  2. OTF Cumulative Threshold sets the desired OTF Cumulative Threshold
  3. Manual will let the user manually specify whether the PSF is Skewed or not
  4. Set Minimum Integral Threshold as needed

8. PSF Detection/Analysis

PSF Detection/Analysis

  1. Mode will decide whether you want to do Analysis Only or both Detection and Analysis
  2. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  3. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  4. Channels should map to your channel patterns
  5. XY Pixel Size is the pixel size in the x and y axes in Microns
  6. Step Size is the actual pixel size in the z axis
  7. Skew Angle is the skew angle of the stage
  8. A deskew will be performed on your input data if the Deskew box is checked
  9. Flip Z Stack will flip the stack in Z if checked
  10. Check Objective Scan if your data is already deskewed
  11. Z Stage Scan should be true if your stage scan is along the z axis
  12. Save as 16 Bit will output data as 16 bit if checked
  13. RWFn are the paths to the Richards and Wolf PSFs
  14. Source String will set a source description for the plots
  15. Bg Factor is the background factor
  16. Master Compute will also use your current node to process cluster jobs if it is checked
  17. Crop Size will set the crop size for the psf
    1. Crop Size is only available when Detection and Analysis is checked
  18. Dist Thresh is for when there are multiple PSFs then you can set the distance threshold between them
    1. Dist Thresh is only available when Detection and Analysis is checked

9. Resample

Resample

  1. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  2. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  3. Resample Factor determines the size to resample the image to
  4. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path.
  5. Interp Method is the interpolation method that will be used
  6. Save as 16 Bit will output data as 16 bit if checked
  7. Input is Zarr should be checked if your input data is in the Zarr format
  8. Large Zarr should be checked if your input data is large scale Zarr data
    1. Only used if using zarr files
  9. Save as Zarr will save your output as Zarr files
  10. The 3D BBox can be set by entering the desired values into the spinboxes
  11. Block Size in Y, X, and Z are the block sizes of each axis
    1. Only used if using zarr files
  12. Batch Size in Y, X, and Z are the batch sizes of each axis
    1. Only used if using zarr files
  13. Border Size in Y, X, and Z are the block sizes of each axis
  14. Parse Cluster will attempt to submit cluster jobs if a scheduler is available
  15. Master Compute will also use your current node to process cluster jobs if it is checked
  16. CPUs Per Task sets the desired number of cores to use for a cluster job
  17. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank
  18. Job Log Dir will set the directory where you would like your job logs to output to (This can usually just be left as is)

10. Tiff/Zarr Converter

Tiff/Zarr Converter

  1. Mode will set whether you want to Convert Tiff files to Zarr files or Zarr files to Tiff files
  2. Refer to section 1.1 in the Main Settings section for instructions on Adding Paths
  3. Refer to section 1.3 in the Main Settings section for instructions on Channel Patterns
  4. Result Dir Name is the Dir where the stitch results will be placed. Just need a name and not the full path
  5. Block Size will determine the chunk size of the output zarr files
  6. Read Whole Tiff will read the entire tiff file to RAM for the conversion when true. When false, the image will be read in blocks to reduce the RAM requirement
  7. Partial File should be true if your tiff files are split into multiple part files
  8. Parse Cluster will attempt to submit cluster jobs if a scheduler is available
  9. CPUs Per Task sets the desired number of cores to use for a cluster job
  10. Use Master Compute Node will also use your current node to process cluster jobs if it is checked
  11. uuid is the unique identifier for jobs when saving the log files. It is fine to leave this blank
  12. Job Log Dir will set the directory where you would like your job logs to output to (This can usually just be left as is)
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