megafish.seqfish module

dog_sds(NA, wavelength, pitch, psf_size_factor=1, dog_sd_factor=1)[source]

Calculates the standard deviations for the Difference of Gaussians (DoG) based on the point spread function (PSF) and imaging parameters.

Parameters:

  • NA (float) – Numerical aperture of the imaging system.

  • wavelength (float) – Wavelength of the fluorescence (in the same units as pitch).

  • pitch (float) – Pixel size or sampling interval (in the same units as wavelength).

  • psf_size_factor (float, optional) – Factor to scale the PSF size; defaults to 1.

  • dog_sd_factor (float, optional) – Factor to scale the second standard deviation for the DoG; defaults to 1.

Returns:

A tuple containing the two standard deviations (dog_sd1, dog_sd2) for the DoG filter.

Return type:

tuple

DoG_filter(zarr_path, group_name, dog_sd1, dog_sd2, axes, mask_radius=None, footer='_dog')[source]

Applies a Difference of Gaussians (DoG) filter to the image data in a Zarr file.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group_name (str) – Group name in the Zarr file where the image data is stored.

  • dog_sd1 (float) – The first standard deviation for the DoG filter.

  • dog_sd2 (float) – The second standard deviation for the DoG filter.

  • axes (list of int) – List of axes along which the filter will be applied.

  • mask_radius (int, optional) – Radius for binary dilation mask to exclude specific regions; defaults to None.

  • footer (str, optional) – Footer string to append to the output group name; defaults to “_dog”.

Returns:

This function saves the filtered data as a new group in the Zarr file.

Return type:

None

local_maxima_footprint(NA, wavelength_um, pitch_um)[source]

Calculates the footprint for detecting local maxima based on the point spread function (PSF) and imaging parameters.

Parameters:

  • NA (float) – Numerical aperture of the imaging system.

  • wavelength_um (float) – Wavelength of the fluorescence (in micrometers).

  • pitch_um (float) – Pixel size or sampling interval (in micrometers).

Returns:

A binary footprint (structuring element) for local maxima detection.

Return type:

numpy.ndarray

local_maxima(zarr_path, group_name, footprint, axes, footer='_lmx')[source]

Detects local maxima in the image data within a Zarr file using a specified footprint.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group_name (str) – Group name in the Zarr file where the image data is stored.

  • footprint (numpy.ndarray) – The structuring element used for detecting local maxima.

  • axes (list of int) – List of axes along which the footprint will be expanded.

  • footer (str, optional) – Footer string to append to the output group name; defaults to “_lmx”.

Returns:

This function saves the detected local maxima as a new group in the Zarr file.

Return type:

None

select_by_intensity_sd(zarr_path, group, sd_factor=0, footer='_isd')[source]

Selects spots in the image data based on intensity, using a threshold defined by the mean intensity and standard deviation.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group (str) – Group name in the Zarr file where the image data is stored.

  • sd_factor (float, optional) – Factor to multiply the standard deviation for the threshold; defaults to 0.

  • footer (str, optional) – Footer string to append to the output group name; defaults to “_isd”.

Returns:

This function saves the filtered data as a new group in the Zarr file.

Return type:

None

select_by_intensity_threshold(zarr_path, group, threshold=0, footer='_ith')[source]

Selects spots in the image data based on a specified intensity threshold.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group (str) – Group name in the Zarr file where the image data is stored.

  • threshold (float, optional) – Intensity threshold for selecting spots; defaults to 0.

  • footer (str, optional) – Footer string to append to the output group name; defaults to “_ith”.

Returns:

This function saves the filtered data as a new group in the Zarr file.

Return type:

None

count_spots(zarr_path, group_spot, group_label, footer='_cnt', delete_chunk_csv=True)[source]

Counts spots within labeled segments in the image data stored in a Zarr file and saves the results as CSV files.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group_spot (str) – Group name for the spot data in the Zarr file.

  • group_label (str) – Group name for the label data in the Zarr file.

  • footer (str, optional) – Footer string to append to the output CSV group name; defaults to “_cnt”.

  • delete_chunk_csv (bool, optional) – Whether to delete temporary chunk CSV files after merging; defaults to True.

Returns:

This function saves the spot counts as CSV files in the csv directory.

Return type:

None

count_summary(zarr_path, groups, group_seg, group_out, channels, genename_path=None)[source]

Summarizes spot counts across multiple groups and cycles, merging the results with segment data and optionally gene names.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • groups (list of str) – List of group names in the Zarr file for which spot counts are available.

  • group_seg (str) – Group name for the segment data.

  • group_out (str) – Output group name for saving the summary CSV.

  • channels (list of int) – List of channels corresponding to each group.

  • genename_path (str, optional) – Path to a CSV file containing gene names for each channel; defaults to None.

Returns:

This function saves the summarized data as a CSV file.

Return type:

None

spot_coordinates(zarr_path, group, footer='_scd')[source]

Extracts coordinates of spots from the image data stored in a Zarr file and saves them as CSV files.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group (str) – Group name in the Zarr file where the spot data is stored.

  • footer (str, optional) – Footer string to append to the output CSV group name; defaults to “_scd”.

Returns:

This function saves the spot coordinates as CSV files.

Return type:

None

spot_intensity(zarr_path, group_spt, group_seg, group_int, footer='_sit')[source]

Computes the intensity of spots within segmented regions for each chunk of the image data and saves the results as CSV files.

Parameters:

  • zarr_path (str) – Path to the Zarr file containing the image data.

  • group_spt (str) – Group name for the spot data in the Zarr file.

  • group_seg (str) – Group name for the segmentation data in the Zarr file.

  • group_int (str) – Group name for the intensity data in the Zarr file.

  • footer (str, optional) – Footer string to append to the output CSV group name; defaults to “_sit”.

Returns:

This function saves the spot intensity data as CSV files.

Return type:

None