Advanced Usage

Email notification

To be emailed when the pipeline crashes or finishes, under basic_info in the config, add the variable email_me with your email address. You must have a sender email with SMTP support, this email's credentials must be given in basic_info under the variables sender_email and sender_email_password.

Generate gene codes

Generate gene codes automatically by:

from coppafish.utils import reed_solomon_codes

codes = reed_solomon_codes(n_gene_codes, n_rounds, n_channels)

where n_gene_codes is the number of gene codes desired, n_rounds is the number of sequencing rounds, and n_channels is the number of channels. An error is thrown if the number of unique gene codes desired is impossible to create. Each channel is labelled 0, 1, 2, ... codes is a dictionary. Each gene code generated can be accessed. For example, to access the first gene code: codes["gene_0"].

Move the output directory

Once a coppafish pipeline is complete or partially complete, the output directory will contain various files. If you wish to move the output directory somewhere else while the notebook already exists, manually copy files to the new output directory (including the notebook). Then use the following command:

from coppafish.utils import set_notebook_output_dir

set_notebook_output_dir("path/to/new/notebook.npz", "new/output_dir")

Note that this will not update the notebook when the tile directory is moved (see here). If the notebook does not exist, it is safe to copy the output directory manually without running the command above.

Move the tile directory

The extracted and filtered images can also be moved to a new tile directory. First, manually move the tile directory to a new location. Then, update the notebook to use the new tile directory by running the command:

from coppafish.utils import set_notebook_tile_dir

set_notebook_tile_dir("path/to/notebook.npz", "path/to/new/tile_dir")

This will only apply the new tile directory to the given notebook. You can run the function multiple times to update every notebook you may have. If no notebook used the old tile directory, you can safely move the directory manually without running the command above.

Retrieve the Notebook config

Notebooks will store a copy of the config file used, this way the notebook becomes separate from the initial starting condition once it has run through the pipeline. To access a notebook's config file:

from coppafish import Notebook

nb = Notebook("path/to/notebook.npz")
config = nb.get_config()

config is a dictionary of dictionaries. Each key is a section/page name, each item is a dictionary containing each config variable and its set value.

Access the absolute file path to the config file by:

nb._config_file

Remove notebook page

Each coppafish section is saved as a separate notebook page. To change the config variables and re-run the coppafish pipeline, you can delete the notebook and all output directory files and re-run again. But, if you only wished to re-run starting from an intermediate section, you can delete all subsequent sections and output files. For example, if you wished to re-run OMP after changing OMP config parameters, you can delete all output files marked omp_* then remove the OMP notebook page by:

from coppafish import Notebook

nb = Notebook("path/to/notebook.npz")
del nb.omp
nb.save()

Now coppafish can be re-run and it will continue from OMP. This is particularly useful for many tile datasets. If you are unsure what must be re-run, then it is suggested to start from an empty output directory.

Skipping bad microscope images

You may have one or more images that are taken which are corrupted, empty, or not as bright as expected. When this happens, the user can manually tell coppafish to run without these images. To do this, specify each tile (t), round (r), channel (c) image by going to your custom config file and add the line

bad_trc = (t1, r1, c1), (t2, r2, c2), ...

under the basic_info section. Each set of brackets represents one image to ignore.