Tilt Series
ts_import
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_import:
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--mdocs REQUIRED Path to the folder containing MDOC files
--pattern Default: *.mdoc. File name pattern to search for in the MDOC
folder
--frameseries REQUIRED Path to a folder containing frame series processing
results and their aligned averages
--tilt_exposure REQUIRED Per-tilt exposure in e-/A^2
--dont_invert Don't invert tilt angles compared to IMOD's convention (inver
sion is usually needed to match IMOD's geometric handedness).
This will flip the geometric handedness
--override_axis Override the tilt axis angle with this value
--auto_zero Adjust tilt angles so that the tilt with the highest average
intensity becomes the 0-tilt
--tilt_offset Subtract this value from all tilt angle values to compensate
pre-tilt
--max_tilt Default: 90. Exclude all tilts above this (absolute) tilt ang
le
--min_intensity Default: 0. Exclude tilts if their average intensity is below
MinIntensity * cos(angle) * 0-tilt intensity; set to 0 to no
t exclude anything
--max_mask Default: 1. Exclude tilts if more than this fraction of their
pixels is masked; needs frame series with BoxNet masking res
ults
--min_ntilts Default: 1. Only import tilt series that have at least this m
any tilts after all the other filters have been applied
-o, --output REQUIRED Path to a folder where the created .tomostar files w
ill be saved
ts_stack
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_stack:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
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--angpix Rescale tilt images to this pixel size; leave out to k
eep the original pixel size
--mask Apply mask to each image if available; masked areas wi
ll be filled with Gaussian noise
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_aretomo
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_aretomo:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
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--angpix Rescale tilt images to this pixel size; normally 10–15
for cryo data; leave out to keep the original pixel s
ize
--mask Apply mask to each image if available; masked areas wi
ll be filled with Gaussian noise
--alignz REQUIRED Value for AreTomo's AlignZ parameter in Angst
rom (will be auto-converted to binned pixels), i.e. th
e thickness of the reconstructed tomogram used for ali
gnments
--axis_iter Default: 0. Number of tilt axis angle refinement itera
tions; each iteration will be started with median valu
e from previous iteration, final iteration will use fi
xed angle
--axis_batch Default: 0. Use only this many tilt series for the til
t axis angle search; only relevant if --axis_iter isn'
t 0
--min_fov Default: 0. Disable tilts that contain less than this
fraction of the tomogram's field of view due to excess
ive shifts
--axis Override tilt axis angle with this value
--patches Number of patches for local alignments in X, Y, separa
ted by 'x': e.g. 6x4. Increases processing time.
--delete_intermediate Delete tilt series stacks generated for AreTomo
--exe Default: AreTomo2. Name of the AreTomo2 executable; mu
st be in $PATH
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_etomo_fiducials
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_etomo_fiducials:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--angpix Rescale tilt images to this pixel size; normally 10–15
for cryo data; leave out to keep the original pixel s
ize
--mask Apply mask to each image if available; masked areas wi
ll be filled with Gaussian noise
--min_fov Default: 0. Disable tilts that contain less than this
fraction of the tomogram's field of view due to excess
ive shifts
--initial_axis Override initial tilt axis angle with this value
--do_axis_search Fit a new tilt axis angle for the whole dataset
--fiducial_size size of gold fiducials in nanometers
--delete_intermediate Delete tilt series stacks generated for ETomo
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_etomo_patches
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_etomo_patches:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--angpix Rescale tilt images to this pixel size; normally 10–15
for cryo data; leave out to keep the original pixel s
ize
--mask Apply mask to each image if available; masked areas wi
ll be filled with Gaussian noise
--min_fov Default: 0. Disable tilts that contain less than this
fraction of the tomogram's field of view due to excess
ive shifts
--initial_axis Override initial tilt axis angle with this value
--do_axis_search Fit a new tilt axis angle for the whole dataset
--patch_size Default: 500. patch size for patch tracking in Angstro
ms
--delete_intermediate Delete tilt series stacks generated for Etomo
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_ctf
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_ctf:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--window Default: 512. Patch size for CTF estimation in binned
pixels
--range_low Default: 30. Lowest (worst) resolution in Angstrom to
consider in fit
--range_high Default: 4. Highest (best) resolution in Angstrom to c
onsider in fit
--defocus_min Default: 0.5. Minimum defocus value in um to explore d
uring fitting (positive = underfocus)
--defocus_max Default: 5. Maximum defocus value in um to explore dur
ing fitting (positive = underfocus)
--voltage Default: 300. Acceleration voltage of the microscope i
n kV
--cs Default: 2.7. Spherical aberration of the microscope i
n mm
--amplitude Default: 0.07. Amplitude contrast of the sample, usual
ly 0.07-0.10 for cryo
--fit_phase Fit the phase shift of a phase plate
--auto_hand Run defocus handedness estimation based on this many t
ilt series (e.g. 10), then estimate CTF with the corre
ct handedness
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_reconstruct
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_reconstruct:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--angpix REQUIRED Pixel size of the reconstructed tomograms in
Angstrom
--halfmap_frames Also produce two half-tomograms, each reconstructed fr
om half of the frames (requires running align_frameser
ies with --average_halves previously)
--halfmap_tilts Also produce two half-tomograms, each reconstructed fr
om half of the tilts (doesn't work quite as well as --
halfmap_frames)
--deconv Also produce a deconvolved version; all half-tomograms
, if requested, will also be deconvolved
--deconv_strength Default: 1. Strength of the deconvolution filter, if r
equested
--deconv_falloff Default: 1. Fall-off of the deconvolution filter, if r
equested
--deconv_highpass Default: 300. High-pass value (in Angstrom) of the dec
onvolution filter, if requested
--keep_full_voxels Mask out voxels that aren't contained in some of the t
ilt images (due to excessive sample shifts); don't use
if you intend to run template matching
--dont_invert Don't invert the contrast; contrast inversion is neede
d for template matching on cryo data, i.e. when the de
nsity is dark in original images
--dont_normalize Don't normalize the tilt images
--dont_mask Don't apply a mask to each tilt image if available; ma
sked areas will be filled with Gaussian noise
--dont_overwrite Don't overwrite existing tomograms in output directory
--subvolume_size Default: 64. Reconstruction is performed locally using
sub-volumes of this size in pixel
--subvolume_padding Default: 3. Padding factor for the reconstruction sub-
volumes (helps with aliasing effects at sub-volume bor
ders)
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_template_match
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_template_match:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--tomo_angpix REQUIRED Pixel size of the reconstructed tomograms in
Angstrom
--template_path Path to the template file
--template_emdb Instead of providing a local map, download the EMDB en
try with this ID and use its main map
--template_angpix Pixel size of the template; leave empty to use value f
rom map header
--template_diameter REQUIRED Template diameter in Angstrom
--template_flip Mirror the template along the X axis to flip the hande
dness; '_flipx' will be added to the template's name
--symmetry Default: C1. Symmetry of the template, e.g. C1, D7, O
--subdivisions Default: 3. Number of subdivisions defining the angula
r search step: 2 = 15° step, 3 = 7.5°, 4 = 3.75° and s
o on
--batch_angles Default: 32. How many orientations to evaluate at once
; memory consumption scales linearly with this; higher
than 32 probably won't lead to speed-ups
--peak_distance Minimum distance (in Angstrom) between peaks; leave em
pty to use template diameter
--npeaks Default: 2000. Maximum number of peak positions to sav
e
--dont_normalize Don't set score distribution to median = 0, stddev = 1
--dont_whiten Don't perform spectral whitening; this can help when t
he alignments are poor by up-weighting lower frequenci
es
--reuse_results Reuse correlation volumes from a previous run if avail
able, only extract peak positions
--check_hand Default: 0. Also try a flipped version of the template
on this many tomograms to see what geometric hand the
y have
--subvolume_size Default: 192. Matching is performed locally using sub-
volumes of this size in pixel
-------------------------------Work distribution--------------------------------
--device_list Space-separated list of GPU IDs to use for processing.
Default: all GPUs in the system
--perdevice Default: 1. Number of processes per GPU
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
-----------------------Advanced remote work distribution------------------------
--workers List of remote workers to be used instead of locally s
pawned processes. Formatted as hostname:port, separate
d by spaces
ts_import_alignments
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_import_alignments:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--alignments REQUIRED Path to a folder containing one sub-folder pe
r tilt series with alignment results from IMOD or AreT
omo
--alignment_angpix REQUIRED Pixel size (in Angstrom) of the images used t
o create the alignments (used to convert the alignment
shifts from pixels to Angstrom)
--min_fov Default: 0. Disable tilts that contain less than this
fraction of the tomogram's field of view due to excess
ive shifts
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.
ts_eval_model
WarpTools - a collection of tools for EM data pre-processing
Version 2.0.0
Showing all available options for command ts_eval_model:
------------------------------Data import settings------------------------------
--settings REQUIRED Path to Warp's .settings file, typically loca
ted in the processing folder. Default file name is 'pr
evious.settings'.
--------------------------------------------------------------------------------
--input_star Path to a STAR file containing custom positions specif
ied using tomoCenteredCoordinate(X/Y/Z)Angst labels. L
eave empty to use a regular grid of positions instead.
--grid_extent Instead of custom positions in --input_star, calculate
an evenly spaced grid with this extent in Angstrom, s
pecified as 'XxYxZ', e.g. 6000x4000x1000.
--grid_dims When calculating an evenly spaced grid, it will have t
his many points in each dimension, specified as 'XxYxZ
', e.g. 30x20x5. The grid spacing will be grid_extent
/ (grid_dims - 1).
--output Output location for the per-tilt series STAR files
----------------------Advanced data import & flow options-----------------------
--input_data Overrides the list of input files specified in the .se
ttings file. Accepts a space-separated list of files,
wildcard patterns, or .txt files with one file name pe
r line.
--input_data_recursive Enables recursive search for files matching the wildca
rd pattern specified in --input_data. Only applicable
when processing and directories are separate. All file
names must be unique.
--input_processing Specifies an alternative directory containing pre-proc
essed results. Overrides the processing directory in t
he .settings file.
--output_processing Specifies an alternative directory to save processing
results. Overrides the processing directory in the .se
ttings file.