Command-Line Help for pineapple

This document contains the help content for the pineapple command-line program.

Command Overview:

• pineapple↴
• pineapple download↴
• pineapple download segmentation↴
• pineapple download benchmark↴
• pineapple download weights↴
• pineapple measure↴
• pineapple measure form↴
• pineapple measure intensity↴
• pineapple measure moments↴
• pineapple measure neural↴
• pineapple measure texture↴
• pineapple measure zernike↴
• pineapple neural↴
• pineapple neural boxes↴
• pineapple neural mask↴
• pineapple neural polygons↴
• pineapple process↴
• pineapple process boxes↴
• pineapple process mask↴
• pineapple process polygons↴
• pineapple profile↴
• pineapple profile boxes↴
• pineapple profile mask↴
• pineapple profile polygons↴
• pineapple utils↴
• pineapple utils images2zarr↴
• pineapple utils mask2boxes↴
• pineapple utils mask2polygons↴

pineapple

Simplified processing for image-based cell profiling with pineapple

Usage: pineapple [NAME] [COMMAND]

Subcommands:

• download — Download standardized bioimaging datasets or pre-trained neural networks.
• measure — Measure quantitative features from bio-imaging data.
• neural — Compute object-level self-supervised features from image and segment pairs.
• process — Extract object-level data from image and segment pairs.
• profile — Compute object-level morphological descriptors from image and segment pairs.
• utils — General utilities for converting and transforming image/image-related data.

Arguments:

• <NAME>

pineapple download

Download standardized bioimaging datasets or pre-trained neural networks.

Usage: pineapple download download segmentation [OPTIONS] download benchmark [OPTIONS] download weights [OPTIONS] download help [COMMAND]...

Subcommands:

• segmentation — Download standardized bioimaging segmentation datasets.
• benchmark — Download standardized single-object benchmark datasets.
• weights — Download pre-trained neural network weights.

pineapple download segmentation

Download standardized bioimaging segmentation datasets.

Usage: pineapple download segmentation [OPTIONS]

Options:

• -n, --name <NAME> — Dataset name. Run pineapple download segmentation --listto see all available datasets. Runpineapple download segementation --all` to download all segmentation datasets
• -o, --output <OUTPUT> — Output path to save downloaded dataset.
• -v, --verbose — Verbose output.
• --list — List all available segmentation datasets.
• --all — Download all available segmentation datasets.

pineapple download benchmark

Download standardized single-object benchmark datasets.

Usage: pineapple download benchmark [OPTIONS]

Options:

• -n, --name <NAME> — Dataset name. Run pineapple download benchmark --listto see all available benchmarks. Runpineapple download benchmark --all` to download all benchmark datasets
• -o, --output <OUTPUT> — Output path to save downloaded dataset.
• -v, --verbose — Verbose output.
• --list — List all available benchmark datasets.
• --all — Download all available benchmark datasets.

pineapple download weights

Download pre-trained neural network weights.

Usage: pineapple download weights [OPTIONS]

Options:

• -n, --name <NAME> — Weights name.
• -v, --verbose — Verbose output.
• --list — List all available neural net weights.
• --all — Download all available neural net weights.

pineapple measure

Measure quantitative features from bio-imaging data.

Usage: pineapple measure measure form [OPTIONS] --polygons <POLYGONS> measure intensity [OPTIONS] --images <IMAGES> measure moments [OPTIONS] --images <IMAGES> measure neural [OPTIONS] --images <IMAGES> measure texture [OPTIONS] --images <IMAGES> measure zernike [OPTIONS] --images <IMAGES> measure help [COMMAND]...

Subcommands:

• form —
• intensity —
• moments —
• neural —
• texture —
• zernike —

pineapple measure form

Usage: pineapple measure form [OPTIONS] --polygons <POLYGONS>

Options:

• -i, --polygons <POLYGONS> — Polygons or polygons directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• --polygon-substring <POLYGON_SUBSTRING> — Substring specifying polygons (e.g. _polygons).
• -t, --threads <THREADS> — Number of threads.

pineapple measure intensity

Usage: pineapple measure intensity [OPTIONS] --images <IMAGES>

Options:

• -i, --images <IMAGES> — Image or image directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image).
• -t, --threads <THREADS> — Number of threads.

pineapple measure moments

Usage: pineapple measure moments [OPTIONS] --images <IMAGES>

Options:

• -i, --images <IMAGES> — Image or image directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image).
• -t, --threads <THREADS> — Number of threads.

pineapple measure neural

Usage: pineapple measure neural [OPTIONS] --images <IMAGES>

Options:

• -i, --images <IMAGES> — Image or image directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq, .npy, .npz).
• -m, --model <MODEL> — Model name.

Default value: dino_vit_small * -d, --device <DEVICE> — Device (cpu, cuda, metal).

Default value: cpu * -v, --verbose — Verbose output. * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * -t, --threads <THREADS> — Number of threads.

pineapple measure texture

Usage: pineapple measure texture [OPTIONS] --images <IMAGES>

Options:

• -i, --images <IMAGES> — Image or image directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image).
• -t, --threads <THREADS> — Number of threads.

pineapple measure zernike

Usage: pineapple measure zernike [OPTIONS] --images <IMAGES>

Options:

• -i, --images <IMAGES> — Image or image directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image).
• -t, --threads <THREADS> — Number of threads.

pineapple neural

Compute object-level self-supervised features from image and segment pairs.

Usage: pineapple neural neural boxes [OPTIONS] --images <IMAGES> --output <OUTPUT> neural mask [OPTIONS] --images <IMAGES> --output <OUTPUT> neural polygons [OPTIONS] --images <IMAGES> --output <OUTPUT> neural help [COMMAND]...

Subcommands:

• boxes —
• mask —
• polygons —

pineapple neural boxes

Usage: pineapple neural boxes [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --boxes <BOXES> — Bounding box directory.
• --device <DEVICE> — Device (cpu, cuda, metal).

Default value: cpu * -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq, .npy, .npz). * -v, --verbose — Verbose output. * -d, --drop-borders — Exclude objects touching edge of image. * -m, --model <MODEL> — Model name.

Default value: dino_vit_small * -p, --pad <PAD> — Add padding around objects before computing self-supervised features.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --box-substring <BOX_SUBSTRING> — Substring specifying bounding boxes (e.g. _boxes). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple neural mask

Usage: pineapple neural mask [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --masks <MASKS> — Mask directory.
• --device <DEVICE> — Device (cpu, cuda, metal).

Default value: cpu * -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq, .npy, .npz). * -v, --verbose — Verbose output. * -d, --drop-borders — Exclude objects touching edge of image. * -m, --model <MODEL> — Model name.

Default value: dino_vit_small * -p, --pad <PAD> — Add padding around objects before computing self-supervised features.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --mask-substring <MASK_SUBSTRING> — Substring specifying masks (e.g. _mask). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple neural polygons

Usage: pineapple neural polygons [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --polygons <POLYGONS> — Polygons directory.
• --device <DEVICE> — Device (cpu, cuda, metal).

Default value: cpu * -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq, .npy, .npz). * -v, --verbose — Verbose output. * -d, --drop-borders — Exclude objects touching edge of image. * -m, --model <MODEL> — Model name.

Default value: dino_vit_small * -p, --pad <PAD> — Add padding around objects before computing self-supervised features.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --polygon-substring <POLYGON_SUBSTRING> — Substring specifying polygons (e.g. _polygons). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple process

Extract object-level data from image and segment pairs.

Usage: pineapple process process boxes [OPTIONS] --images <IMAGES> --output <OUTPUT> process mask [OPTIONS] --images <IMAGES> --output <OUTPUT> process polygons [OPTIONS] --images <IMAGES> --output <OUTPUT> process help [COMMAND]...

Subcommands:

• boxes —
• mask —
• polygons —

pineapple process boxes

Usage: pineapple process boxes [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --boxes <BOXES> — Bounding boxes directory.
• -o, --output <OUTPUT> — Output directory.
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. One or more of c (complete pixels) and/or x (bounding boxes).

Default value: cx * -p, --pad <PAD> — Add padding around extracted objects

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --box-substring <BOX_SUBSTRING> — Substring specifying boxes (e.g. _boxes). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -e, --image-format <IMAGE_FORMAT> — Format to save extracted object images (e.g. png, jpeg, npy).

Default value: png * -a, --array-format <ARRAY_FORMAT> — Format to save extracted polygons and/or bounding boxes (e.g. json).

Default value: json * -t, --threads <THREADS> — Number of threads.

pineapple process mask

Usage: pineapple process mask [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --masks <MASKS> — Mask directory.
• -o, --output <OUTPUT> — Output directory.
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. One or more of c (complete pixels), f (foreground pixels), b (background pixels), m (binary mask), p (polygons), and x (bounding boxes).

Default value: cm * -p, --pad <PAD> — Add padding around extracted objects

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --mask-substring <MASK_SUBSTRING> — Substring specifying masks (e.g. _mask). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -e, --image-format <IMAGE_FORMAT> — Format to save extracted object images (e.g. png, jpeg, npy).

Default value: png * -a, --array-format <ARRAY_FORMAT> — Format to save extracted polygons and/or bounding boxes (e.g. json).

Default value: json * -t, --threads <THREADS> — Number of threads.

pineapple process polygons

Usage: pineapple process polygons [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --polygons <POLYGONS> — Polygons directory.
• -o, --output <OUTPUT> — Output directory.
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. One or more of c (complete pixels), f (foreground pixels), b (background pixels), m (binary mask), p (polygons), and x (bounding boxes).

Default value: cm * -p, --pad <PAD> — Add padding around extracted objects

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --polygon-substring <POLYGON_SUBSTRING> — Substring specifying polygons (e.g. _polygon). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -e, --image-format <IMAGE_FORMAT> — Format to save extracted object images (e.g. png, jpeg, npy).

Default value: png * -a, --array-format <ARRAY_FORMAT> — Format to save extracted polygons and/or bounding boxes (e.g. json).

Default value: json * -t, --threads <THREADS> — Number of threads.

pineapple profile

Compute object-level morphological descriptors from image and segment pairs.

Usage: pineapple profile profile boxes [OPTIONS] --images <IMAGES> --output <OUTPUT> profile mask [OPTIONS] --images <IMAGES> --output <OUTPUT> profile polygons [OPTIONS] --images <IMAGES> --output <OUTPUT> profile help [COMMAND]...

Subcommands:

• boxes —
• mask —
• polygons —

pineapple profile boxes

Usage: pineapple profile boxes [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --boxes <BOXES> — Bounding boxes directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. Compute descriptors across one or more features including c (complete pixels) and/or x (bounding boxes).

Default value: cx * -p, --pad <PAD> — Add padding around extracted objects before computing profiles.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --box-substring <BOX_SUBSTRING> — Substring specifying bounding boxes (e.g. _boxes). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple profile mask

Usage: pineapple profile mask [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --masks <MASKS> — Mask directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. Compute descriptors across one or more features including c (complete pixels), f (foreground pixels), b (background pixels), m (binary mask), p (polygons), and x (bounding boxes).

Default value: cm * -p, --pad <PAD> — Add padding around extracted objects before computing profiles.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --mask-substring <MASK_SUBSTRING> — Substring specifying masks (e.g. _mask). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple profile polygons

Usage: pineapple profile polygons [OPTIONS] --images <IMAGES> --output <OUTPUT>

Options:

• -i, --images <IMAGES> — Image directory.
• -s, --polygons <POLYGONS> — Polygons directory.
• -o, --output <OUTPUT> — Output directory or file (.csv, .txt, .tsv, .pq).
• -v, --verbose — Verbose output.
• -d, --drop-borders — Exclude objects touching edge of image.
• -m, --mode <MODE> — Mode. Compute descriptors across one or more features including c (complete pixels), f (foreground pixels), b (background pixels), m (binary mask), p (polygons), and x (bounding boxes).

Default value: cm * -p, --pad <PAD> — Add padding around extracted objects before computing profiles.

Default value: 1 * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * --polygon-substring <POLYGON_SUBSTRING> — Substring specifying polygons (e.g. _polygons). * --min-size <MIN_SIZE> — Exclude objects smaller than a minimum size.

Default value: 1 * -t, --threads <THREADS> — Number of threads.

pineapple utils

General utilities for converting and transforming image/image-related data.

Usage: pineapple utils utils images2zarr [OPTIONS] --images <IMAGES> --output <OUTPUT> --resize-width <RESIZE_WIDTH> --resize-height <RESIZE_HEIGHT> --channels <CHANNELS> utils mask2boxes [OPTIONS] --mask <MASK> --output <OUTPUT> utils mask2polygons [OPTIONS] --mask <MASK> --output <OUTPUT> utils help [COMMAND]...

Subcommands:

• images2zarr —
• mask2boxes —
• mask2polygons —

pineapple utils images2zarr

Usage: pineapple utils images2zarr [OPTIONS] --images <IMAGES> --output <OUTPUT> --resize-width <RESIZE_WIDTH> --resize-height <RESIZE_HEIGHT> --channels <CHANNELS>

Options:

• -i, --images <IMAGES> — Image directory.
• -o, --output <OUTPUT> — Output zarr file.
• --resize-width <RESIZE_WIDTH> — Resize each image to specified width.
• --resize-height <RESIZE_HEIGHT> — Resize each image to specified height.
• --channels <CHANNELS> — Number of image channels.
• --dtype <DTYPE> — Cast subpixels to specified data type (u8, u16, u32, f32, or f64).

Default value: f32 * --gzip-compression <GZIP_COMPRESSION> — Gzip compression level (0 - 9)

Default value: 5 * -v, --verbose — Verbose output. * --image-substring <IMAGE_SUBSTRING> — Substring specifying images (e.g. _image). * -t, --threads <THREADS> — Number of threads.

pineapple utils mask2boxes

Usage: pineapple utils mask2boxes [OPTIONS] --mask <MASK> --output <OUTPUT>

Options:

• -i, --mask <MASK> — Mask or mask directory.
• -o, --output <OUTPUT> — Output bounding boxes file.
• -v, --verbose — Verbose output.
• --mask-substring <MASK_SUBSTRING> — Substring specifying masks (e.g. _mask).
• -t, --threads <THREADS> — Number of threads.

pineapple utils mask2polygons

Usage: pineapple utils mask2polygons [OPTIONS] --mask <MASK> --output <OUTPUT>

Options:

• -i, --mask <MASK> — Mask or mask directory.
• -o, --output <OUTPUT> — Output polygons file.
• -v, --verbose — Verbose output.
• --mask-substring <MASK_SUBSTRING> — Substring specifying masks (e.g. _mask).
• -t, --threads <THREADS> — Number of threads.

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