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Welcome to the demo page of PAIS/PIDB queries.

All the queries are executed upon PAIS database and Pathology Image Database (PIDB).

The output format can be changed by setting the format parameter. For text result, format can be HTML (format=html, default), XML (format=xml), or JSON (format=json).

If the output is an image, the format can be JPEG (format=jpg), P$NG(format=png, default) or GIF(format=gif). The format of a tile image can be tif (format=tif).

All the parameters are seperated by ";", and can be adjusted.

The Web APIs are documented in PAIS Web APIs

PAIS Queries


List Queries

  1. Get all PAIS UIDs in PAIS database (HTML). Example: /pais/list/paisuids
  2. Get all PAIS UIDs in PAIS database (XML). Example: /pais/list/paisuids;format=xml
  3. Get all PAIS UIDs in PAIS database (CSV). Example: /pais/list/paisuids;format=csv
  4. Get all image UIDs in PAIS database. Example: /pais/list/imageuids
  5. Get all slide UIDs in PAIS database. Example: /pais/list/slideuids
  6. Get all patient UIDs in PAIS database. Example: /pais/list/slideuids

Markup Queries

Density:
  1. Get markup (nuclear) density of a tile. Example: /pais/markups/density/tile;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384
  2. Get markup (nuclear) density of a image. Example: /pais/markups/density/image;imageuid=TCGA-27-1836-01Z-DX2_20x;method=NS-MORPH;seqno=1
  3. Get markup (nuclear) density of a PAIS document. Example: /pais/markups/density/document;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;format=html
  4. Get all markup (nuclear) density grouped by image. Example: /pais/markups/density/groupbyimage
  5. Get all markup (nuclear) density grouped by PAISUID. Example: /pais/markups/density/groupbydocument
Boundaries:
  1. Get markup (nuclear) boundaries of a tile. Example: /pais/markups/boundaries/tile;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384;format=svg
  2. Get markup (nuclear) boundaries in a window (SVG). Example: /pais/markups/boundaries/window;imageuid=TCGA-27-1836-01Z-DX2_20x;x=4096;y=16384;w=600;h=600;samplingrate=3;format=svg
  3. Get markup (nuclear) boundaries in a polygon. Example: /pais/markups/boundaries/polygon;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384;polygon="4096 16384,4496 16384,4496 20384,4096 20384,4096 16384";samplingrate=1;format=html";samplingrate=1;format=svg
  4. Get markup (nuclear) boundaries of a point. Example: /pais/markups/boundaries/containingpoint;imageuid=TCGA-27-1836-01Z-DX2_20x;x=300;y=300;
  5. Get markup (nuclear) boundaries of intersections of 2 PAIS documents containing the same tile name. Example: /pais/markups/boundaries/intersection;tilename=gbm1.1-0000040960-0000040960;paisuid1=gbm1.1_40x_20x_NS-MORPH_1;paisuid2=gbm1.1_40x_20x_NS-MORPH_2
Centroids:
  1. Get markup centroids of a tile. Example: /pais/markups/centroids/tile;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384
  2. Get markup centroids of a window. Example: /pais/markups/centroids/window;imageuid=TCGA-27-1836-01Z-DX2_20x;x=4096;y=16384;w=300;h=300
  3. Get markup centroids of a polygon. Example: /pais/markups/centroids/polygon;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384;polygon="4096 16384,4496 16384,4496 20384,4096 20384,4096 16384"

Document Queries

Document:
  1. Return PAIS document (zipped XML format) of a tile. Example: /pais/documents/tile;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384

Feature Queries

Basic features:
  1. Return all features from a tile. Example: /pais/features/tile;paisuid=TCGA-15-1448-01Z-00-DX1_20x_20x_NS-MORPH_1;tilename=TCGA-15-1448-01Z-00-DX1-0000040960-0000032768
  2. Return feature histogram image of a document. Example: /pais/features/histogram;paisuid=TCGA-02-0001-01Z-00-DX1_20x_20x_NS-MORPH_1;feature=area;width=1200;height=700;format=PNG
Aggregation features:
  1. Return all feature aggregation of a document. Example: /pais/features/aggregation/document;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1
  2. Return all feature aggregation of an image. Example: /pais/features/aggregation/image;imageuid=TCGA-27-1836-01Z-DX2_20x
  3. Return all feature aggregation of a patient. Example: /pais/features/aggregation/patient;patientuid=0187

PIDB Queries


List Queries

List Queries:
  1. List all image uids in the database (HTML). Example: /images/list/imageuids
  2. List all image uids of a patient. Example: /images/list/imageuids;patientid=0152
  3. List all tilenames of an image. Example: /images/list/tilenames;imageuid=TCGA-06-0152-01Z-00-DX6_20x
  4. List all tilenames of a tileset. Example: /images/list/tilenames;tilset=1
  5. Return the tilename which contains a point. Example: /images/list/tilenameofpoint;imageuid=TCGA-06-0152-01Z-00-DX6_20x;x=12289;y=5000

Image queries

Image queries:
  1. Download a tile image. Example: /images/image/tile;tilename=TCGA-06-0152-01Z-00-DX6-0000016384-0000004096;format=tif
  2. Download the image contained in a window. Example: /images/image/window;imageuid=TCGA-27-1836-01Z-DX2_20x;x=17706;y=2844;w=800;h=800;format=PNG
  3. Download a whole slide image. Example: /images/image/wsi;imageuid=TCGA-27-1836-01Z-DX2_20x
  4. Retrieve the dimension of a whole slide image. Example: images/image/dimension;imagereferenceuid=TCGA-06-0152-01Z-00-DX6_20x;format=csv
  5. Retrieve the coordinates of all tiles of a whole slide image. Example: images/image/tiling/positions;imagereferenceuid=TCGA-06-0152-01Z-00-DX6_20x;width=4096;height=4096;format=csv
Thumbnail queries:
  1. Visualize thumbnail of a tile. Example: /images/thumbnail/tile;tilename=TCGA-06-0152-01Z-00-DX6-0000016384-0000004096
  2. Visualize thumbnail of a whole slide image. Example: /images/thumbnail/wsi;imageuid=TCGA-27-1836-01Z-DX2_20x
Overlay queries:
  1. Visualize markups on top of a tile image. Example: /images/overlay/tile;paisuid=TCGA-27-1836-01Z-DX2_20x_20x_NS-MORPH_1;tilename=TCGA-27-1836-01Z-DX2-0000004096-0000016384
  2. Visualize markups on top of a window image. Example: /images/overlay/window;imageuid=TCGA-27-1836-01Z-DX2_20x;x=4096;y=16384;w=800;h=800;samplingrate=3;format=jpg
Similarity queries:
  1. Visualize region icons of all similar objects (based on mean features) for a document. Example: /images/similarity/feature;paisuid=TCGA-06-0195-01Z-00-DX5_20x_20x_NS-MORPH_1;rowsize=5;format=png
  2. Visualize region icons of all similar objects (based on nuclear clustering label) for a document. Example: /images//tcga/images/similarity/cluster;imageuid=TCGA-02-0010-01Z-00-DX3_20x;label=2;rowsize=10;format=png