Creating a Volume¶
This section reviews how to organize images for import into a volume and what operations can be performed on the volume.
The build manager places data from various platforms into a single volume directory. Users use the “nornir_build” command and provide a path to the volume’s directory to run specific operations on the volume:
nornir-build <volumepath> <Command> ...
Importing data¶
The first command for any Nornir volume:
nornir-build <volumepath> <import_command> <inputpath>
For example nornir-build Y:/Volumes/RC2 ImportIDOC Y:/Captures/RC2/ will instruct Nornir to check the Y:/Captures/RC2 directory for sections and import any that it can find into the volume stored in Y:/Volumes/RC2
The import command extends volumes non-destructively provided different sections are not assigned the same number. Import can be run repeatedly as now sections become available.
Organizing data for import¶
Nornir needs the data to be laid out in a predictable fashion. No spaces are allowed in nornir folder names!
The convention nornir uses is for a directory to exist for the volume with a numbered subdirectory for each mosaic. The directory name should contain the section number, and optionally an underscore followed by the name of the section.
<experimentfolder>/<section#>_[sectionname]
Sometimes it is just useful to organize multiple mosaics into a single volume even though they aren’t a 3D volume. In this case just invent different section numbers for each capture. For example lets say I capture three mosaics in SerialEM (which produces an .idoc meta-data file) for Bob’s eggplant and he had some ID #’s he wants to make sure get carried along with the data.
Bob
0001_EggID4567
capture.idoc
001.tif
002.tif
…
1245.tif
0002_EggID7645
…
The result will two sections named “EggID4567” and “EggID7645” respectively.
Notes¶
Often we want to carry more data forward. The existing importers extract a lot of scope settings from the meta-data files. If you want to record additional data, for example the box Bob’s samples are stored in, this can be put into a notes.txt file and saved in the 0001_EggID4567. The file will copied along with the section.
Bob
0001_EggID4567
capture.idoc
…
Notes.txt
0002_EggID7645
Extending the importer¶
Nornir has an .xml file mapping extensions to importers. It examines each directory for extensions and if the extensions are found it will attempt to load the python module specified in the xml file and pass it the directory containing the files with matching extensions.
Platform Scripts¶
For SerialEM and Surveyor there are canned windows batch files for building TEM volumes and brightfield microscopy volumes respectively. These are tailored for the Marc Lab’s workflow as needed, but can be a reference for development. Scripts are run from the scripts directory of your Python installation.
Transmission Electron Microscopy via SerialEM¶
Import SerialEM .idoc files and remove tiles without enough features:
TEMPrepare <volume path> <import path>Build mosaics and produce a report for SerialEM TEM:
TEMBuild <volume path>Align the slices into a single volume:
TEMAlign <volume path>
Brightfield Microscopy via Surveyor¶
Import .pmg files, correct non-DAPI channels using brightfield shading correction:
CMPBuild <volume path> <import path>Align the slices into a single volume:
CMPAlign <volume path>
Pipelines¶
Nornir defines different pipelines that manipulate the volume. Pipelines are defined in a pipeline.xml file and can be edited by advanced users.
Builds tend to have many steps in common. The Marc lab builds TEM images with this pipeline:
Prune
AdjustContrast
Mosaic
Assemble
MosaicReport
CreateBlobFilter
AlignSections -Downsample 32
RefineSectionAlignment -Downsample 32
RefineSectionAlignment -Downsample 32 16
SliceToVolume
ScaleVolumeTransform 16 -> 1
Sample batch files can be found in the scripts directory, which is copied to the python scripts directory at setup time. TEMPrepare, TEMBuildMosaic, and TEMAlign show the commands used to build the RC2 TEM volume at the Marc lab.
Note: Certain arguments support regular expressions. See the python re module for instructions on how to construct appropriate regular expressions.
Options available to all build commands. Specific pipelines may extend the argument list.
usage: nornir_build volumepath [-h] [-debug] [-lowpriority] [-verbose]
volumepath
{RecoverLinks,RecoverNotes,AddStos,AddToStosMap,AdjustContrast,AlignSections,Assemble,AssembleStosOverlays,AssembleTiles,AssembleTilesFromImage,CalculateStosGroupWarpMetrics,Cleanup,CleanupStos,CopyStosGroup,CreateBlobFilter,CreateStosGroup,CreateVikingXML,ExportImages,ExportMetadata,Histogram,ImportDM4,ImportIDoc,ImportImages,ImportMRC,ImportPMG,InvertFilter,ListBlockStosMaps,ListDamagedSections,ListFilterContrast,ListGroupSectionMappings,ListMissingTilesets,ListPruneCutoff,ListStosGroups,ListStosMap,MarkSectionsDamaged,MarkSectionsUndamaged,Mosaic,MosaicNoTranslate,MosaicReport,MosaicToVolume,PrintContrast,Prune,RefineSectionAlignment,RemoveFromStosMap,RemoveStosGroup,RenameFilter,ReportVolumeBounds,ScaleVolumeTransforms,SelectBestRegistrationChain,SetContrast,SetFilterLock,SetFilterMaskName,SetMosaicLock,SetPruneCutoff,ShadeCorrect,SliceToVolume,StosReport,VolumeImage}
...
Positional Arguments¶
- volumepath
Directory containing volume to execute command on
options¶
- -debug
If true any exceptions raised by pipelines are not handled.
Default: False
- -lowpriority, -lp
Run the build with lower priority. The machine may be more responsive at the expense of much slower builds. 3x-5x slower in tests.
Default: False
- -verbose
Provide additional output
Default: False
Sub-commands:¶
RecoverLinks¶
Used to recover missing meta-data. This searches child directories for VolumeData.xml files and re-links them to the parent element in volume path. This command does not recurse and does not need to be run on the top-level volume directory.
nornir_build volumepath RecoverLinks [-h] [-save]
options¶
- -save
Set this flag to save the VolumeData.xml files with the located linked elements included.
Default: False
RecoverNotes¶
Used to recover or update notes files in a folder. This searches a path for *.txt files and creates/updates a notes element with the information in the file.
nornir_build volumepath RecoverNotes [-h] [-save]
options¶
- -save
Set this flag to save the VolumeData.xml files with the located linked elements included.
Default: False
AddStos¶
Import a Slice-to-slice transformation to a StosGroup.
nornir_build volumepath AddStos [-h] [-to [TO ...]] [-cc [CC ...]] -File
INPUTSTOSFULLPATH [-Block BLOCKNAME]
-StosGroup STOSGROUP -ControlSection
CONTROLSECTION -ControlChannel CONTROLCHANNEL
-ControlFilter CONTROLFILTER
-ControlDownsample CONTROLDOWNSAMPLE
-MappedSection MAPPEDSECTION -MappedChannel
MAPPEDCHANNEL -MappedFilter MAPPEDFILTER
-MappedDownsample MAPPEDDOWNSAMPLE -Type TYPE
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -File
Path to the .stos file to import
- -Block
Block to create the StosGroup within
Default: “TEM”
- -StosGroup
Name of the StosGroup
- -ControlSection
Control Section Number of the Stos Transform
- -ControlChannel
Control Channel of the Stos Transform
- -ControlFilter
Control Filter of image used for transform
- -ControlDownsample
Downsample level of controlled section’s image
- -MappedSection
Mapped Section Number of the Stos Transform
- -MappedChannel
Mapped Channel of the Stos Transform
- -MappedFilter
Mapped Filter of image used for transform
- -MappedDownsample
Downsample level of mapped section’s image
- -Type
Name of the StosGroup
AddToStosMap¶
List all SliceToSlice mappings within a stos map
nornir_build volumepath AddToStosMap [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKNAME] -Name STOSMAPNAME
-ControlSection CONTROLSECTION
-MappedSection MAPPEDSECTION
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Name
Name of the StosMap
- -ControlSection
Control Section Number
- -MappedSection
Mapped Section Number
AdjustContrast¶
Creates a new filter with adjusted contrast. The cutoffs can be adjusted within the meta-data by altering the AutoLevelHint element of the input filters volume.xml meta-data file.
nornir_build volumepath AdjustContrast [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-Gamma GAMMA] [-MinCutoff MINCUTOFF]
[-MaxCutoff MAXCUTOFF] -InputFilter
INPUTFILTER
[-OutputFilter OUTPUTFILTER]
[-OutputBpp OUTPUTBPP] -InputTransform
INPUTTRANSFORM
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Gamma
Gamma value for intensity auto-level
- -MinCutoff
Min pixel intensity cutoff as a percentage, 0 to 100
Default: 0.1
- -MaxCutoff
Max pixel intensity cutoff as a percentage, 0 to 100. Specifying ‘1’ puts the cutoff at 99% of the maximum pixel intensity value.
Default: 0.5
- -InputFilter
Filter to draw images from
Default: “Raw8”
- -OutputFilter
Filter to draw images from
Default: “Leveled”
- -OutputBpp
Bits-per-pixel of output filter images
- -InputTransform
Mosaic transform to prune. The transform provides the list of tiles in the mosaic.
Default: “Prune”
AlignSections¶
Performs slice to slice alignment from scratch to produce an initial 3D volume. After alignment the best alignment results are selected to create a final stosmap.
nornir_build volumepath AlignSections [-h] [-to [TO ...]] [-cc [CC ...]]
[-Center CENTER]
[-NumAdjacentSections NUMADJACENTSECTIONS]
[-AngleRange ANGLESEARCHRANGE]
[-Channels CHANNELSREGEX]
[-Filters FILTERSREGEX] [-UseMasks]
-Downsample STOSBRUTEDOWNSAMPLE
[-OutputStosMap OUTPUTSTOSMAP]
[-NoFlipCheck]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Center
Center section of the volume. Defaults to center if unspecified. The first run center is saved in meta-data and re-used on later runs.
- -NumAdjacentSections
Number of adjacent sections to attempt registration with.
Default: 1
- -AngleRange
Range of angles to check in degrees not radians
Default: “”
- -Channels
Regular expression describing channels to be aligned
Default: “*”
- -Filters
Regular expression describing filters to be aligned
Default: “(?![M|m]ask)”
- -UseMasks
Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
Default: False
- -Downsample
Amount to downsample input images before attempting alignment. Images are padded to the next power of two for the FFT. Large images, roughly greater than 2048x2048, can be very slow.
Default: 1
- -OutputStosMap
Name assigned to generated stos map.
Default: “PotentialRegistrationChain”
- -NoFlipCheck
Do not check for flipped sections. Use this option if it is impossible for images to be flipped. Doubles execution speed.
Default: False
Assemble¶
Creates an assembled image from a transform and filter. Optionally creates a new channel for output.
nornir_build volumepath Assemble [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS] [-Downsample LEVELS]
[-NoInterlace] [-Channels CHANNELREGEX]
[-ChannelPrefix OUTPUTCHANNELPREFIX]
[-Filters FILTERREGEX]
[-Transform TRANSFORMNAME] [-Crop CROPBOX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Downsample
Comma separated list of downsample levels for assembling images. If output is desired only one downsample level can be used.
Default: 1
- -NoInterlace
Setting this flag skips the interlace step after assemble. Interlaced images load faster on web pages, but are larger than non-interlaced images.
Default: True
- -Channels
Regular expression describing channels to be assembled
Default: “*”
- -ChannelPrefix
Create a new channel for the output with this prefix and the name of the input.
Default: “”
- -Filters
Regular expression describing filters to be assembled
Default: “(?![M|m]ask)”
- -Transform
Directory to move assembled images to
Default: “Grid”
- -Crop
Bounding box of region to assemble. Default is no cropping. Form is MinX,MinY,MaxX,MaxY with no spaces.
Default: “”
AssembleStosOverlays¶
Assembles registered images for .stos files in a group. Typically this is done so quality of registration at that stage can be assessed.
nornir_build volumepath AssembleStosOverlays [-h] [-to [TO ...]]
[-cc [CC ...]] -StosGroup
STOSGROUP -Downsample
INPUTDOWNSAMPLE -StosMap STOSMAP
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Stos group to assemble
Default: “StosBrute”
- -Downsample
Downsample level to assemble
- -StosMap
Name assigned to generated stos map.
Default: “FinalStosMap”
AssembleTiles¶
Build small full-resolution tiles, usually 256x256, that allow regions of the mosaic to be rapidly loaded
nornir_build volumepath AssembleTiles [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
[-Transform TRANSFORMNAME]
[-HighestDownsample HIGHESTDOWNSAMPLE]
[-Shape SHAPE]
[-MaxWorkingImageArea MAX_TEMP_IMAGE_AREA]
[-IgnoreStale]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be assembled
Default: “*”
- -Filters
Regular expression describing filters to be assembled
Default: “(?![M|m]ask)”
- -Transform
Transform defining images into mosaic
Default: “Grid”
- -HighestDownsample
Highest level downsample to generate. Defaults to the level required to show entire section on one tile.
- -Shape
The size the tiles passed as a comma-delimited pair of integers. For example 256,512. If a single number is passed it is used for both dimensions
Default: 256,256
- -MaxWorkingImageArea
Determines the amount of memory the system should use to generate the tiles. Suggested value is total system memory in bytes divided by four
- -IgnoreStale
Setting this flag skips testing existing tiles to ensure they were created after the input transform.
Default: False
AssembleTilesFromImage¶
Build small full-resolution tiles, usually 256x256, that allow regions of the mosaic to be rapidly loaded. Uses the filter image as source instead of transforms.
nornir_build volumepath AssembleTilesFromImage [-h] [-to [TO ...]]
[-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
[-HighestDownsample HIGHESTDOWNSAMPLE]
[-Shape SHAPE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be assembled
Default: “*”
- -Filters
Regular expression describing filters to be assembled
Default: “(?![M|m]ask)”
- -HighestDownsample
Highest level downsample to generate. Defaults to the level required to show entire section on one tile.
- -Shape
The size the tiles passed as a comma-delimited pair of integers. For example 256,512. If a single number is passed it is used for both dimensions
Default: 512,512
CalculateStosGroupWarpMetrics¶
Creates images indicating the amount of warping present in each .stos file in a group. Typically this is done so quality of registration at that stage can be assessed.
nornir_build volumepath CalculateStosGroupWarpMetrics [-h] [-to [TO ...]]
[-cc [CC ...]]
-StosGroup STOSGROUP
-Downsample
INPUTDOWNSAMPLE -StosMap
STOSMAP
[-MaxAngle MAXREPORTEDANGLE]
[-RenderToTargetSection]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Stos group to assemble
Default: “StosBrute”
- -Downsample
Downsample level to assemble
- -StosMap
Name assigned to generated stos map.
Default: “FinalStosMap”
- -MaxAngle
Maximum angle value, in degrees, in output image heatmaps. Defaults to max angle found for each section. Specify a value to ensure consistent heatmap ranges for each transform. 15-30 degrees is usually a reasonable value.
- -RenderToTargetSection
Indicates whether the image is rendered in the source or target section coordinates. Rendering to source will result in a square image. Rendering to target is better for transforms to volume space.
Default: True
Cleanup¶
Clean common errors from the volume meta-data
nornir_build volumepath Cleanup [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
CleanupStos¶
Clean common errors in section mappings
nornir_build volumepath CleanupStos [-h] [-to [TO ...]] [-cc [CC ...]]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
CopyStosGroup¶
Create a SliceToSlice transform group
nornir_build volumepath CopyStosGroup [-h] [-to [TO ...]] [-cc [CC ...]]
-Input SOURCEGROUPNAME -Output
TARGETGROUPNAME [-Block BLOCKNAME]
[-Downsample DOWNSAMPLE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Input
Source StosGroup to copy transforms from.
- -Output
Target StosGroup to copy transform to.
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Downsample
Downsample level of stos files
Default: 1
CreateBlobFilter¶
Create a blob filter from an input filter. Blobbing can make brute slice-to-slice alignment more reliable for downsampled mosaics with fine textures.
nornir_build volumepath CreateBlobFilter [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELREGEX] -InputFilter
INPUTFILTER
[-Levels BLOBDOWNSAMPLELEVELS]
[-Radius BLOBRADIUS]
[-Median BLOBMEDIAN] [-Max BLOBMAX]
[-OutputFilter OUTPUTFILTERNAME]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section to execute blob on. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be assembled
Default: “*”
- -InputFilter
Name of filter to create blob filter for
Default: “Leveled”
- -Levels
Downsample levels to be blobbed
Default: 1
- -Radius
Radius to calculate variance within
Default: 9
- -Median
Median filter radius for input
Default: 7
- -Max
Max variance before cropping
Default: 3
- -OutputFilter
Prefix added to created filters
Default: “Blob”
CreateStosGroup¶
Create a SliceToSlice transform group
nornir_build volumepath CreateStosGroup [-h] [-to [TO ...]] [-cc [CC ...]]
-StosGroup STOSGROUP
[-Block BLOCKNAME]
[-Downsample DOWNSAMPLE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Name of the StosGroup to create
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Downsample
Downsample level of stos files
Default: 1
CreateVikingXML¶
Create a vikingxml file for use in Viking
nornir_build volumepath CreateVikingXML [-h] [-to [TO ...]] [-cc [CC ...]]
[-StosGroup STOSGROUP]
[-StosMap STOSMAP] [-Host HOST]
-OutputFile OUTPUTFILE
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Stos group to pull images from. If not specified only unregistered mosaics are included.
- -StosMap
Slice-to-slice mapping of transforms. If not specified only unregistered mosaics are included.
- -Host
Url of volume, overrides the about.xml settings
- -OutputFile
Name of file to write .VikingXML is appended to name automatically
ExportImages¶
Copies images of sections to an output directory
nornir_build volumepath ExportImages [-h] [-to [TO ...]] [-cc [CC ...]]
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
[-Downsample DOWNSAMPLE]
[-Output OUTPUTPATH]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Channels
Regular expression describing channels to be assembled
Default: “*”
- -Filters
Regular expression describing filters to be assembled
Default: “(?![M|m]ask)”
- -Downsample
Downsample output images by this factor
Default: 1
- -Output
Directory to move assembled images to
ExportMetadata¶
Export all meta-data to a single file
nornir_build volumepath ExportMetadata [-h] [-to [TO ...]] [-cc [CC ...]]
[-Output OUTPUTPATH]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Output
Full path of output xml file, defaults to VolumeData.SingleFileBackup.xml in the Volume directory.
Histogram¶
Calculates the histogram from all tiles in a mosaic
nornir_build volumepath Histogram [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-Filters FILTERSREGEX] -InputTransform
INPUTTRANSFORM [-Downsample DOWNSAMPLE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Filters
Regular expression describing filters to include, * processes all filters
Default: “(?![M|m]ask)”
- -InputTransform
The transform provided the list of tiles in the mosaic.
Default: “Prune”
- -Downsample
Use downsampled tiles for faster histogram calculation
Default: 1
ImportDM4¶
Import Digital Micrograph 4
nornir_build volumepath ImportDM4 [-h] [-to [TO ...]] [-cc [CC ...]]
[-ext EXTENSION] [-Sections SECTIONS]
[-overlap TILE_OVERLAP]
ImportDir
Positional Arguments¶
- ImportDir
Directory to import from
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -ext
Extension of digital micrograph version 4 files, default is dm4
Default: “dm4”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -overlap
Overlap of tiles as a percentage, either a single value or a comma-delimited pair (X%,Y%).ntex: 15 would be a 15 overlap on both axis.ntex: 10,20 would be a 10% X overlap and 20% Y overlap.
ImportIDoc¶
Import SerialEM IDOC into a volume.
nornir_build volumepath ImportIDoc [-h] [-to [TO ...]] [-cc [CC ...]]
[-ext EXTENSION] [-Min MINVALUE]
[-Max MAXVALUE] [-Sections SECTIONS]
[-CameraBpp CAMERABPP]
ImportDir
Positional Arguments¶
- ImportDir
Directory to import from. The .idoc files in subdirectories should be named with the desired section number after import. i.e. 0005.idoc to import the file as section #5.
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -ext
Extension of idoc files, default is idoc
Default: “idoc”
- -Min
Min intensity cutoff. A value from 0.0 to 1.0
Default: 0.0001
- -Max
Max intensity cutoff. A value from 0.0 to 1.0
Default: 0.9999
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -CameraBpp
The actual bits-per-pixel of the camera. Limits the range of image histograms being expanded beyond reason due to errors in input image data or meta-data.
ImportImages¶
Import single images that represent an entire section in a volume
nornir_build volumepath ImportImages [-h] [-to [TO ...]] [-cc [CC ...]] -Scale
SCALEVALUEINNM [-ext EXTENSION]
ImportDir
Positional Arguments¶
- ImportDir
Directory to import from
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Scale
Pixel size in nanometers
- -ext
Extension of image files, default is png
Default: “png”
ImportMRC¶
Import SerialEM MRC files into a volume.
nornir_build volumepath ImportMRC [-h] [-to [TO ...]] [-cc [CC ...]]
[-ext EXTENSION] [-CameraBpp CAMERABPP]
ImportDir
Positional Arguments¶
- ImportDir
Directory to import from. The .mrc files in subdirectories should be named with the desired section number after import. i.e. 0005.mrc to import the file as section #5.
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -ext
Extension of mrc files, default is mrc
Default: “mrc”
- -CameraBpp
The actual bits-per-pixel of the camera. Limits the range of image histograms being expanded beyond reason due to errors in input image data or meta-data.
ImportPMG¶
Import PMG file into a volume
nornir_build volumepath ImportPMG [-h] [-to [TO ...]] [-cc [CC ...]] -Scale
SCALEVALUEINNM [-ext EXTENSION]
ImportDir
Positional Arguments¶
- ImportDir
Directory to import from. The PMG file should follow this format: Slide#_Block#_Section#_Initials_Mag_Spot_Probe. However only Section and Probe are used as the section number and channel name respectively. The rest is stored as meta-data.
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Scale
Pixel size in nanometers
- -ext
Extension of pmg files, default is pmg
Default: “pmg”
InvertFilter¶
Produce a new filter, inverted from the input
nornir_build volumepath InvertFilter [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX] -InputFilter
FILTERSREGEX -OutputFilter OUTPUTFILTER
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -InputFilter
The filter to invert
- -OutputFilter
Prefix added to output filters
Default: “Inverted”
ListBlockStosMaps¶
List all SliceToSlice maps in a block
nornir_build volumepath ListBlockStosMaps [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKNAME]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Name of block
Default: “TEM”
ListDamagedSections¶
Print a list of all damaged sections. Damaged sections are never used as control sections when chaining slice-to-slice transforms together to build slice-to-volume transforms
nornir_build volumepath ListDamagedSections [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Regular expression describing blocks to include, * processes all blocks
Default: “*”
ListFilterContrast¶
Print a list of the contrast settings used for all sections.
nornir_build volumepath ListFilterContrast [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-Filters FILTERSREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Filters
Regular expression describing filters to include, * processes all filters
Default: “(?![M|m]ask)”
ListGroupSectionMappings¶
List all SliceToSlice transform groups
nornir_build volumepath ListGroupSectionMappings [-h] [-to [TO ...]]
[-cc [CC ...]]
[-Block BLOCKNAME] -StosGroup
STOSGROUP -Downsample
DOWNSAMPLE
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Block to create the StosGroup within
Default: “TEM”
- -StosGroup
Name of the StosGroup
- -Downsample
Downsample level of stos files
ListMissingTilesets¶
Print a list of filters without tilesets
nornir_build volumepath ListMissingTilesets [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-Filters FILTERSREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Filters
Regular expression describing filters to include, * processes all filters
Default: “*”
ListPruneCutoff¶
List the prune thresholds set for a filter
nornir_build volumepath ListPruneCutoff [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
[-header_fill HEADER_FILL]
[-fill VALUE_FILL]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]. Defaults to every section
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Filters
Regular expression describing filters to be edited
Default: “*”
- -header_fill
The amount of padding to use for names in the list
Default: 12
- -fill
The amount of padding to use for prune values in the list
Default: 6
ListStosGroups¶
List all SliceToSlice transform groups
nornir_build volumepath ListStosGroups [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKNAME]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Block to create the StosGroup within
Default: “TEM”
ListStosMap¶
List all SliceToSlice mappings within a stos map
nornir_build volumepath ListStosMap [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKNAME] -Name STOSMAPNAME
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Name
Name of the StosMap
MarkSectionsDamaged¶
Mark sections as damaged. Damaged sections are never used as control sections when chaining slice-to-slice transforms together to build slice-to-volume transforms
nornir_build volumepath MarkSectionsDamaged [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKREGEX]
[-Sections SECTIONS]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Regular expression describing blocks to include, * processes all blocks
Default: “*”
- -Sections
Section numbers that should not be used as control sections. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
MarkSectionsUndamaged¶
Remove sections from the damaged list. Damaged sections are never used as control sections when chaining slice-to-slice transforms together to build slice-to-volume transforms
nornir_build volumepath MarkSectionsUndamaged [-h] [-to [TO ...]]
[-cc [CC ...]]
[-Block BLOCKREGEX]
[-Sections SECTIONS]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Regular expression describing blocks to include, * processes all blocks
Default: “*”
- -Sections
Section numbers to remove from the damaged list. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
Mosaic¶
Aligns tiles of a filter into a single mosaic. Produces an assembled mosaic image.
nornir_build volumepath Mosaic [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS] [-Channels CHANNELSREGEX]
[-RegistrationDownsample DOWNSAMPLE]
-InputFilter INPUTFILTER
[-InputTransform INPUTTRANSFORMNAME]
[-OutputTransform OUTPUTTRANSFORMNAME]
[-RefineIterations REFINEITERATIONS]
[-Threshold DISPLACEMENTTHRESHOLD]
[-MinOverlap MIN_OVERLAP]
[-ExpandOverlapScalar EXCESS_SCALAR]
[-first_pass_inter_tile_distance FIRST_PASS_INTER_TILE_DISTANCE]
[-inter_tile_distance INTER_TILE_DISTANCE]
[-MinFeatureScore FEATURE_SCORE_THRESHOLD]
[-MinTranslateIterations MIN_TRANSLATE_ITERATIONS]
[-RelaxIterations MAX_RELAX_ITERATIONS]
[-OffsetChangeTolerance OFFSET_ACCEPTANCE_THRESHOLD]
[-RelaxThreshold MAX_RELAX_TENSION_CUTOFF]
[-CellArea CELLAREA]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -RegistrationDownsample
Downsample level to use for ir-tools
Default: 4
- -InputFilter
Filter to use for registration
Default: “Raw8”
- -InputTransform
Name of the input transform
Default: “Prune”
- -OutputTransform
Name of output transform.
Default: “Grid”
- -RefineIterations
Maximum number of refinement passes to run
Default: 10
- -Threshold
Displacement threshold for control point movement (in pixels). Refinement stops below this value
Default: 0.25
- -MinOverlap
Minimum amount of overlap tiles must have to contribute to the final mosaic.
Default: 0.08
- -ExpandOverlapScalar
How much additional area should we pad the overlapping regions with.
Default: 1.0
- -first_pass_inter_tile_distance
A value from 0 to 1 that scales the distance between the centers of the two tiles. A value of 0 considers the full images when registering. A value of 1.0 only considers the overlapping regions according to the tile transforms. Reduce this value in the first registration pass to increase the search area.
Default: 1
- -inter_tile_distance
A value from 0 to 1 that scales the distance between the centers of the two tiles. A value of 0 considers the full images when registering. A value of 1.0 only considers the overlapping regions according to the tile transforms. Reduce this value in early registration passes to increase the search area.
Default: 1
- -MinFeatureScore
Minimum average FFT power spectral density. Determines if overlapping have enough texture for registration to be accurate.
Default: 0.35
- -MinTranslateIterations
Minimum number of iterations phase correlation and relaxation
Default: 5
- -RelaxIterations
Maximum number of relaxation passes to in translation only placement phase
Default: 500
- -OffsetChangeTolerance
Do not re-register (recalculate phase correlation of) a pair of overlapping tiles if the change in overlap position compared to the previous iteration is less than this distance in pixels.
Default: 1
- -RelaxThreshold
Stop iteration of relaxation phase if the maximum tension vector on any tile is below this value (in pixels).
Default: 0.1
- -CellArea
Size of region around each grid point to register, in pixels
Default: 128
MosaicNoTranslate¶
Aligns tiles of a filter into a single mosaic. Produces an assembled mosaic image. Assumes stage coordinates are correct and refines distortions only without translating tiles.
nornir_build volumepath MosaicNoTranslate [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-RegistrationDownsample DOWNSAMPLE]
[-RefineIterations REFINEITERATIONS]
[-CellArea CELLAREA]
[-Threshold DISPLACEMENTTHRESHOLD]
[-MaxOffset MAXOFFSET] -InputFilter
INPUTFILTER
[-InputTransform INPUTTRANSFORMNAME]
[-OutputTransform OUTPUTTRANSFORMNAME]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -RegistrationDownsample
Downsample level to use for ir-tools
Default: 4
- -RefineIterations
Maximum number of refinement passes to run
Default: 10
- -CellArea
Size of region around each grid point to register, in pixels
Default: 128
- -Threshold
Displacement threshold for control point movement (in pixels). Refinement stops below this value
Default: 0.1
- -MaxOffset
Comma separated list of downsample levels used for assembling output images
Default: 0.5
- -InputFilter
Filter to use for registration
Default: “Raw8”
- -InputTransform
Name of the input transform
Default: “Prune”
- -OutputTransform
Name of output transform.
Default: “Grid”
MosaicReport¶
Generate a web page summarizing the output of 2D section mosaics. Includes prune scores, contrast histograms, and assembled images if any.
nornir_build volumepath MosaicReport [-h] [-to [TO ...]] [-cc [CC ...]]
[-PruneFilter PRUNEFILTER]
[-ContrastFilter CONTRASTFILTER]
[-AssembleFilter ASSEMBLEFILTER]
[-AssembleDownsample ASSEMBLEDOWNSAMPLE]
[-Output OUTPUTPATH]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -PruneFilter
Input filter passed to Prune pipeline
Default: “Raw8”
- -ContrastFilter
Input filter passed to Adjust Contrast pipeline
Default: “Raw8”
- -AssembleFilter
Input filter passed to Assemble or Mosaic pipeline
Default: “Raw8”
- -AssembleDownsample
Downsample level to build assembled image thumbnails from
Default: 1
- -Output
Name of report html file
Default: “ImageReport.html”
MosaicToVolume¶
Used after slice to volume. Creates new mosaic transforms that map tiles directly into the volume space. This is done by passing the mosaic transform through a slice-to-volume transformation. Assemble can then be used to produce volume registered images.
nornir_build volumepath MosaicToVolume [-h] [-to [TO ...]] [-cc [CC ...]]
[-Channels CHANNELSREGEX]
[-InputDownsample STOSDOWNSAMPLE]
[-InputMap INPUTMAPNAME]
[-InputGroup INPUTSTOSGROUP]
[-InputTransform INPUTTRANSFORMNAME]
[-OutputTransform OUTPUTTRANSFORM]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Channels
Regular expression describing channels to be processed
Default: “*”
- -InputDownsample
Downsample level of input stosgroup
Default: 1
- -InputMap
Name of output group
Default: “SliceToVolume”
- -InputGroup
Name of stos group to pass mosaic transforms through
Default: “SliceToVolume”
- -InputTransform
Mosaic transform to pass through slice-to-slice transform
Default: “Grid”
- -OutputTransform
Name of output transform mapping a channel to a volume
Default: “ChannelToVolume”
PrintContrast¶
Print the contrast parameters for a filter
nornir_build volumepath PrintContrast [-h] [-to [TO ...]] [-cc [CC ...]]
-Sections SECTIONS
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Filters
Regular expression describing filters to be edited
Default: “*”
Prune¶
Removes tiles without enough features for proper alignment.
nornir_build volumepath Prune [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS] [-Channels CHANNELSREGEX]
-Threshold PRUNETHRESHOLD
[-InputFilter INPUTFILTER]
[-Downsample DOWNSAMPLE]
[-InputTransform INPUTTRANSFORM]
[-OutputTransform OUTPUTTRANSFORM]
[-overlap OVERLAP]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Threshold
Texture complexity threshold
Default: 0
- -InputFilter
Filter to calculate complexity upon
Default: “Raw8”
- -Downsample
Tiles are downsampled by this factor before being scored
Default: 1
- -InputTransform
Mosaic transform to prune. The transform provides the list of tiles in the mosaic.
Default: “Stage”
- -OutputTransform
Name of output transform. Contains tiles from input transform minus tiles below threshold.
Default: “Prune”
- -overlap
Percentage overlap between tiles, 0.0 to 1,0
Default: 0.1
RefineSectionAlignment¶
Refines slice-to-slice alignment at the given downsample level. This pipeline is often used iteratively at higher and higher resolutions to improve registration quality.
nornir_build volumepath RefineSectionAlignment [-h] [-to [TO ...]]
[-cc [CC ...]]
[-SectionMap STOSMAP]
[-InputGroup INPUTGROUP]
-InputDownsample
INPUTDOWNSAMPLE
[-OutputGroup OUTPUTGROUP]
-OutputDownsample
OUTPUTDOWNSAMPLE
[-Filters FILTERSREGEX]
[-UseMasks]
[-Threshold DISPLACEMENTTHRESHOLD]
[-Spacing GRIDSPACING]
[-CellArea CELLAREA]
[-Iterations ITERATIONS]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -SectionMap
Map describing which sections register to each other
Default: “FinalStosMap”
- -InputGroup
Map describing which sections register to each other
Default: “StosBrute”
- -InputDownsample
Downsample level to use for input
- -OutputGroup
Name of output group
Default: “StosGrid”
- -OutputDownsample
Downsample level to use for refinement
- -Filters
Regular expression describing filters to be aligned
Default: “(?![M|m]ask)”
- -UseMasks
Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
Default: False
- -Threshold
Displacement threshold for control point movement. Refinement stops below this value
Default: 0.1
- -Spacing
Grid spacing in pixels
Default: 128
- -CellArea
Size of region around each grid point to register, in pixels
Default: 256
- -Iterations
Maximum number of refinement passes to run
Default: 10
RemoveFromStosMap¶
List all SliceToSlice mappings within a stos map
nornir_build volumepath RemoveFromStosMap [-h] [-to [TO ...]] [-cc [CC ...]]
[-Block BLOCKNAME] -Name STOSMAPNAME
-ControlSection CONTROLSECTION
-MappedSection MAPPEDSECTION
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Name
Name of the StosMap
- -ControlSection
Control Section Number
- -MappedSection
Mapped Section Number
RemoveStosGroup¶
Remove a SliceToSlice transform group
nornir_build volumepath RemoveStosGroup [-h] [-to [TO ...]] [-cc [CC ...]]
-StosGroup STOSGROUP
[-Block BLOCKNAME]
[-Downsample DOWNSAMPLE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Name of the StosGroup to remove
- -Block
Block to create the StosGroup within
Default: “TEM”
- -Downsample
Downsample level of stos files
Default: 1
RenameFilter¶
Renames a filter
nornir_build volumepath RenameFilter [-h] [-to [TO ...]] [-cc [CC ...]]
-InputFilter INPUTFILTER -OutputFilter
NEWNAME
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -InputFilter
Old Filter name
- -OutputFilter
New Filter name
ReportVolumeBounds¶
Generate a web page summarizing the output of 2D section mosaics. Includes prune scores, contrast histograms, and assembled images if any.
nornir_build volumepath ReportVolumeBounds [-h] [-to [TO ...]] [-cc [CC ...]]
-Channels CHANNELREGEX -Transforms
TRANSFORMSREGEX [-StosMap STOSMAP]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Channels
Regular expression describing channels to be assembled
- -Transforms
Transform defining images into mosaic
- -StosMap
Slice-to-slice mapping of transforms. If not specified only unregistered mosaics are included.
ScaleVolumeTransforms¶
Scales a stos group to use a different downsample level. Useful for producing full-resolution output after generating transforms using downsampled images.
nornir_build volumepath ScaleVolumeTransforms [-h] [-to [TO ...]]
[-cc [CC ...]] -InputGroup
SCALEGROUPNAME -InputDownsample
SCALEINPUTDOWNSAMPLE
[-OutputDownsample SCALEOUTPUTDOWNSAMPLE]
[-UseMasks]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -InputGroup
Name of stos group to scale
- -InputDownsample
Downsample level of input stosgroup
- -OutputDownsample
Downsample level of output. Defaults to 1.
Default: 1
- -UseMasks
Use masks for images if they are available. Masked areas are replaced with random noise for alignment purposes.
Default: False
SelectBestRegistrationChain¶
Create a new registration chain by examining the stos overlays produced by AssembleStosOverlays. If two registrations are possible for a section the overlay with the most overlap is chosen.
nornir_build volumepath SelectBestRegistrationChain [-h] [-to [TO ...]]
[-cc [CC ...]] -StosGroup
STOSGROUP -Downsample
INPUTDOWNSAMPLE
-InputStosMap INPUTSTOSMAP
[-OutputStosMap OUTPUTSTOSMAP]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Stos group to assemble
Default: “StosBrute”
- -Downsample
Downsample level to assemble
- -InputStosMap
Name assigned to generated stos map.
Default: “PotentialRegistrationChain”
- -OutputStosMap
Name assigned to generated stos map.
Default: “FinalStosMap”
SetContrast¶
Set the contrast parameters for a filter
nornir_build volumepath SetContrast [-h] [-to [TO ...]] [-cc [CC ...]]
[-Min MINVALUE] [-Max MAXVALUE]
[-Gamma GAMMAVALUE] -Sections SECTIONS
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Min
Min intensity value, set to 0 in output
Default: NaN
- -Max
Max intensity value, set to 1 in output
Default: NaN
- -Gamma
Gamma adjustment
Default: NaN
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Filters
Regular expression describing filters to be edited
Default: “*”
SetFilterLock¶
Toggle the locked flag for a filter. Locked filters will not have images recalculated.
nornir_build volumepath SetFilterLock [-h] [-to [TO ...]] [-cc [CC ...]]
-Locked LOCKED -Sections SECTIONS
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Locked
Lock value, 0 = unlocked, 1 = locked
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Filters
Regular expression describing filters to be edited
Default: “*”
SetFilterMaskName¶
Specify another filter in the same channel to use as a mask when using this filter.
nornir_build volumepath SetFilterMaskName [-h] [-to [TO ...]] [-cc [CC ...]]
-InputFilter INPUTFILTER -MaskName
NEWNAME
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -InputFilter
Old Filter name
- -MaskName
New Mask Name for filter name
SetMosaicLock¶
Toggle the locked flag for a .mosaic transform to prevent or enable regeneration.
nornir_build volumepath SetMosaicLock [-h] [-to [TO ...]] [-cc [CC ...]]
-Locked LOCKED -Sections SECTIONS
[-Channels CHANNELREGEX] -Transforms
TRANSFORMREGEX
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Locked
Lock value, 0 = unlocked, 1 = locked
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Transforms
Regular expression describing transform names to be edited
SetPruneCutoff¶
Set the prune threshold for a filter
nornir_build volumepath SetPruneCutoff [-h] [-to [TO ...]] [-cc [CC ...]]
-Value PRUNEVAL -Sections SECTIONS
[-Channels CHANNELREGEX]
[-Filters FILTERREGEX]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Value
Prune threshold to set
Default: 0
- -Sections
Section numbers to edit. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to be edited
Default: “*”
- -Filters
Regular expression describing filters to be edited
Default: “*”
ShadeCorrect¶
Brightfield microscopy shading correction. Uses the max tile intensity across all tiles to determine the shading gradient. Produces an inverted output filter with the shading subtracted.
nornir_build volumepath ShadeCorrect [-h] [-to [TO ...]] [-cc [CC ...]]
[-Sections SECTIONS]
[-Channels CHANNELSREGEX]
[-Filters FILTERSREGEX]
[-OutputFilter OUTPUTFILTER] -Correction
{brightfield,darkfield}
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Sections
Section numbers to process. If omitted all sections are processed. Values are separated with commas and ranges are indicated by hyphens. Ex: ‘1,3,5-7’ == [1,3,5,6,7]
- -Channels
Regular expression describing channels to include, * processes all channels
Default: “*”
- -Filters
Regular expression describing filters to include, * processes all filters
Default: “(?![M|m]ask)”
- -OutputFilter
Prefix added to output filters
Default: “ShadingCorrected”
- -Correction
Possible choices: brightfield, darkfield
Brightfield images have a light background with darker features. Darkfield images have a dark background with light features.
Default: “brightfield”
SliceToVolume¶
Created a group of slice-to-volume transforms from a group of slice-to-slice transforms
nornir_build volumepath SliceToVolume [-h] [-to [TO ...]] [-cc [CC ...]]
[-Downsample STOVDOWNSAMPLE] -InputGroup
STOVINPUTGROUP
[-OutputGroup STOVOUTPUTGROUPNAME]
[-InputMap INPUTMAP]
[-OutputMap OUTPUTMAP] [-NoEnrichment]
[-Tolerance TOLERANCE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -Downsample
Downsample level to use for SliceToVolume
Default: 16
- -InputGroup
Map describing which sections register to each other
Default: “StosGrid”
- -OutputGroup
Name of output group
Default: “SliceToVolume”
- -InputMap
Name of output group
Default: “FinalStosMap”
- -OutputMap
Name of output registration map. Defaults to -OutputGroup name if omitted.
- -NoEnrichment
Do not add extra control points to slice-to-volume transforms to increase accuracy.
Default: True
- -Tolerance
Maximum distance, at full resolution, between the expected and actual position of transformed triangle centroids. Above this value a control point is added at the centroid to increase transform accuracy.
Default: 64
StosReport¶
Generate a web page containing a summary of the alignments between sections in a 3D volume
nornir_build volumepath StosReport [-h] [-to [TO ...]] [-cc [CC ...]]
-StosGroup STOSGROUP [-Output OUTPUTPATH]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -StosGroup
Stos group to pull images from
- -Output
Name of report html file
Default: “StosReport.html”
VolumeImage¶
Produces an assembled image for transforms in a stos group. If the transforms are slice-to-volume transforms the output should be registered into a volume. Note that using this function requires assembled images to exist at full resolution. If these do not exist see the MosaicToVolume pipeline.
nornir_build volumepath VolumeImage [-h] [-to [TO ...]] [-cc [CC ...]]
[-InputGroup VOLUMEIMAGEGROUPNAME]
[-InputDownsample VOLUMEIMAGEDOWNSAMPLE]
options¶
- -to
E-Mail addresses for reports
Default: “”
- -cc
E-Mail addresses for reports
Default: “”
- -InputGroup
Name of stos group to create scaled version of, default = SliceToVolume
Default: “SliceToVolume”
- -InputDownsample
Downsample level of input stosgroup, default = 1
Default: 1