Command Reference

tapqir

Bayesian analysis of co-localization single-molecule microscopy image data.

Initialize Tapqir in the working directory. Initializing a Tapqir workspace creates a .tapqir sub-directory for storing config.yaml file, loginfo file, and files that are created by commands such as tapqir fit.

tapqir [OPTIONS] COMMAND [ARGS]...

Options

--cd <cd>

Change working directory.

--version

Show Tapqir version and exit.

--install-completion <install_completion>

Install completion for the specified shell.

Options:

bash | zsh | fish | powershell | pwsh

--show-completion <show_completion>

Show completion for the specified shell, to copy it or customize the installation.

Options:

bash | zsh | fish | powershell | pwsh

dwelltime

tapqir dwelltime [OPTIONS]

Options

--model <model>

Tapqir model

Default:

cosmos

Options:

cosmos | crosstalk | cosmos+hmm

-K <K>

Number of exponentials

Default:

3

--cuda, --cpu

Run computations on GPU or CPU

-n, --num-samples <num_samples>

Number of posterior samples

Default:

500

-it, --num-iter <num_iter>

Number of iterations

Default:

10000

--progress-bar <progress_bar>

fit

Fit the data to the selected model.

Available models:

• cosmos: multi-color time-independent co-localization model.

• cosmos+hmm: multi-color hidden markov co-localization model.

• crosstalk: multi-color time-independent co-localization model with cross-talk.

tapqir fit [OPTIONS]

Options

--model <model>

Tapqir model

Default:

cosmos

Options:

cosmos | crosstalk | cosmos+hmm

-S, --num-states <S>

Number of spot states

Default:

1

--cuda, --cpu

Run computations on GPU or CPU

-n, --nbatch-size <nbatch_size>

AOI batch size

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'nbatch-size')

-f, --fbatch-size <fbatch_size>

Frame batch size

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'fbatch-size')

-lr, --learning-rate <learning_rate>

Learning rate

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'learning-rate')

-it, --num-iter <num_iter>

Number of iterations

Default:

0

-k, --k-max <k_max>

Maximum number of spots per image

Default:

2

--matlab

Save parameters in matlab format

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'matlab')

--funsor, --pyro

Use funsor or pyro backend

Default:

False

--pykeops, --no-pykeops

Use pykeops backend for offset marginalization

Default:

True

-w, --overwrite

Overwrite defaults values.

Default:

True

--no-input

Disable interactive prompt.

Default:

False

--progress-bar <progress_bar>

glimpse

Extract AOIs from raw glimpse images.

Analyzing data acquired with Glimpse and pre-processed with the imscroll program will require the following files:

• image data in glimpse format and header file

• aoiinfo file designating the locations of target molecules (on-target AOIs) in the binder channel

• (optional) aoiinfo file designating the off-target control locations (off-target AOIs) in the binder channel

• driftlist file recording the stage movement that took place during the experiment

tapqir glimpse [OPTIONS]

Options

--dataset <dataset>

Dataset name

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'dataset')

-P, --aoi-size <P>

AOI image size - number of pixels along the axis

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'P')

--offset-x <offset_x>

x-axis position of the top-left corner of the offset region

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'offset-x')

--offset-y <offset_y>

y-axis position of the top-left corner of the offset region

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'offset-y')

--offset-P <offset_P>

Offset region size - number of pixels along the axis

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'offset-P')

--bin-size <bin_size>

Offset histogram bin size (odd number)

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'bin-size')

--frame-range, --no-frame-range

Specify frame range.

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'frame-range')

--frame-start <frame_start>

Starting frame.

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'frame-start')

--frame-end <frame_end>

Ending frame.

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'frame-end')

--use-offtarget, --no-use-offtarget

Use off-target AOI locations.

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'use-offtarget')

-C, --num-channels <num_channels>

Number of color channels

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'num-channels')

--name <name>

--glimpse-folder <glimpse_folder>

--driftlist <driftlist>

--ontarget-aoiinfo <ontarget_aoiinfo>

--offtarget-aoiinfo <offtarget_aoiinfo>

-w, --overwrite

Overwrite defaults values.

Default:

True

--no-input

Disable interactive prompt.

Default:

False

-l, --labels

Add on-target binding labels.

Default:

False

--progress-bar <progress_bar>

log

Show logging info.

tapqir log [OPTIONS]

show

tapqir show [OPTIONS]

Options

--model <model>

Tapqir model

Default:

cosmos

Options:

cosmos | crosstalk | cosmos+hmm

--n <n>

n

Default:

0

--f1 <f1>

--f2 <f2>

--show-fov, --no-show-fov

Default:

True

--gui <gui>

stats

tapqir stats [OPTIONS]

Options

--model <model>

Tapqir model

Default:

cosmos

Options:

cosmos | crosstalk | cosmos+hmm

--cuda, --cpu

Run computations on GPU or CPU

-n, --nbatch-size <nbatch_size>

AOI batch size

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'nbatch-size')

-f, --fbatch-size <fbatch_size>

Frame batch size

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'fbatch-size')

--matlab

Save parameters in matlab format

Default:

functools.partial(<function get_default at 0x7f2efe1020e0>, 'matlab')

--funsor, --pyro

Use funsor or pyro backend

Default:

False

--no-input

Use defaults values.

Default:

False

subset

Create a new dataset from the subset of AOIs indicated in aoi_subset.txt file.

tapqir subset [OPTIONS]

ttfb

tapqir ttfb [OPTIONS]

Options

--model <model>

Tapqir model

Default:

cosmos

Options:

cosmos | crosstalk | cosmos+hmm

--binary, --probabilistic

Plot a binary or probabilistic rastergram

Default:

False

--cuda, --cpu

Run computations on GPU or CPU

-n, --num-samples <num_samples>

Number of posterior samples

Default:

2000

-it, --num-iter <num_iter>

Number of iterations

Default:

15000

--progress-bar <progress_bar>