Buildmanager (nornir_buildmanager)

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:

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