megafish.segment module

watershed_label(zarr_path, group, min_distance, footer='_wts')[source]

Applies watershed segmentation to the image data.

Parameters:

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

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

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

  • min_distance (int) – Minimum distance between peaks in the distance map.

Returns:

The function saves the segmented result to a new Zarr group.

Return type:

None

dilation(zarr_path, group, mask_radius, footer='_dil')[source]

Applies a binary dilation operation to the image data.

Parameters:

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

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

  • mask_radius (int) – Radius of the structuring element used for dilation.

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

Returns:

The function saves the dilated result to a new Zarr group.

Return type:

None

merge_split_label(zarr_path, group, footer='_msl')[source]

Merges split labels in an image dataset by applying offsets and resolving conflicts.

Parameters:

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

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

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

Returns:

The function saves the merged label dataset to a new Zarr group.

Return type:

None

grow_voronoi(zarr_path, group, depth, max_distance, footer='_vor')[source]

Expands labeled regions in an image using a Voronoi-like approach, filling the image based on the nearest labeled pixel within a specified maximum distance.

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.

  • depth (int) – The depth of overlap used when applying the Voronoi expansion across chunks.

  • max_distance (float) – The maximum allowable distance for a pixel to be filled based on the nearest label.

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

Returns:

This function saves the expanded Voronoi regions as a new Zarr group.

Return type:

None

masking(zarr_path, group_target, group_mask, reverse=False, footer='_msk')[source]

Applies a mask to the target image data, setting values outside the mask to zero.

Parameters:

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

  • group_target (str) – Group name in the Zarr file for the target data to be masked.

  • group_mask (str) – Group name in the Zarr file for the mask data.

  • reverse (bool, optional) – If True, inverts the mask, setting values within the mask to zero; defaults to False.

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

Returns:

This function saves the masked result as a new Zarr group.

Return type:

None

fill_holes(zarr_path, group, footer='_fil')[source]

Fills holes in labeled regions of an image dataset.

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.

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

Returns:

This function saves the image with filled holes as a new Zarr group.

Return type:

None

remove_edge_mask(zarr_path, group, footer='_egr')[source]

Removes labeled regions touching the edges of the image.

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.

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

Returns:

This function saves the image with edge labels removed as a new Zarr group.

Return type:

None

label_edge(zarr_path, group, thickness, footer='_edg')[source]

Identifies and labels the edges of labeled regions in an image dataset, with adjustable thickness.

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.

  • thickness (int) – Thickness of the labeled edges.

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

Returns:

This function saves the image with labeled edges as a new Zarr group.

Return type:

None

repeat_cycle(zarr_path, group, n_cycle, footer='_rep')[source]

Repeats an image dataset over multiple cycles.

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.

  • n_cycle (int) – Number of times to repeat the dataset over cycles.

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

Returns:

This function saves the repeated dataset as a new Zarr group.

Return type:

None

info_csv(zarr_path, group, pitch, footer='_seg')[source]

Generates segment information CSV files from image data stored in a Zarr file, summarizing properties such as area and centroid for each segment. Merges the CSV files into a single summary.

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.

  • pitch (tuple of float) – Pixel size in (y, x) directions, used to convert pixel measurements to micrometers.

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

Returns:

This function saves the segment information as CSV files.

Return type:

None

merge_groups(zarr_path, groups, output_group)[source]

Merges multiple groups of image data from a Zarr file into a single output group.

Parameters:

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

  • groups (list of str) – List of group names in the Zarr file to merge.

  • output_group (str) – The name of the output group where the merged data will be saved.

Returns:

This function saves the merged dataset as a new group in the Zarr file.

Return type:

None

normalize_groups(zarr_path, group, footer='_nrm')[source]

Normalizes intensity values across groups within an image dataset and computes the maximum intensity projection (MIP).

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.

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

Returns:

This function saves the normalized and MIP result as a new Zarr group.

Return type:

None

select_slice(zarr_path, group, dim, position, chunk_dict, footer='sel')[source]

Selects a slice from an image dataset along a specified dimension.

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.

  • dim (str) – The dimension along which to select the slice (e.g., “z”, “cycle”).

  • position (int) – The index position of the slice to select along the specified dimension.

  • chunk_dict (dict or None) – A dictionary specifying chunk sizes for each dimension. If None, the original chunk sizes (excluding the selected dimension) are used.

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

Returns:

This function saves the selected slice as a new Zarr group.

Return type:

None

merge_to_one_group(zarr_path, groups, output_group)[source]

Merges multiple groups of image data from a Zarr file into a single output group.

Parameters:

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

  • groups (list of str) – List of group names in the Zarr file to merge.

  • output_group (str) – The name of the output group where the merged data will be saved.

Returns:

This function saves the merged dataset as a new group in the Zarr file.

Return type:

None

scaled_mip(zarr_path, group, dim='cycle', footer='_nrm')[source]

Normalizes intensity values across a specified dimension and computes the maximum intensity projection (MIP).

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.

  • dim (str, optional) – The dimension along which to compute the MIP; defaults to “cycle”.

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

Returns:

This function saves the normalized and MIP result as a new Zarr group.

Return type:

None