extraction.rst

Single-cell identification

bigfish.multistack

Functions to exploit detection and segmentation results, by identifying individual cells and their objects.

Identify and remove transcription sites

Define transcription sites as clustered RNAs detected inside nucleus:

• bigfish.multistack.remove_transcription_site

More generally, identify detected objects within a specific cellular region:

• bigfish.multistack.identify_objects_in_region

remove_transcription_site

identify_objects_in_region

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Define and export single-cell results

Extract detection and segmentation results and for every individual cell:

• bigfish.multistack.extract_cell
• bigfish.multistack.extract_spots_from_frame
• bigfish.multistack.summarize_extraction_results

See an example of application here <https://github.com/fish-quant/big-fish- examples/blob/master/notebooks/6%20-%20Extract%20cell%20level%20results.ipynb>.

extract_cell

extract_spots_from_frame

summarize_extraction_results

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Manipulate surfaces, coordinates and boundaries

Convert identified surfaces into coordinates, delimit boundaries and manipulates coordinates:

• bigfish.multistack.center_mask_coord
• bigfish.multistack.from_boundaries_to_surface
• bigfish.multistack.from_surface_to_boundaries
• bigfish.multistack.from_binary_to_coord
• bigfish.multistack.complete_coord_boundaries
• bigfish.multistack.from_coord_to_frame
• bigfish.multistack.from_coord_to_surface

center_mask_coord

from_boundaries_to_surface

from_surface_to_boundaries

from_binary_to_coord

complete_coord_boundaries

from_coord_to_frame

from_coord_to_surface