MSI-Ptolemy API information for developers¶

Square_Finding node:¶

The square finding should operate on each gr image tile at its saved mrc dimension.

1. Shell script to call and specified in Blobs settings.
2. Output json file is a list of square blob founds by the algorithm. For each item, it requires the following key, value pairs.

area: integer¶

number of pixels the square opening on the gr tile image.

center: [float, float]¶

The coordinate of the square opening center [col, row] with [0,0] at the start of the data block in the mrc image.

score: float¶

The score of the blob as goodness of the blob as a good square. The higher the number the better.

brightness: float¶

Mean intensity value or equivalent in the square blob. This is saved as a part of statistics but not used for filtering.

vertices: [[float, float], [float, float], [float, float], .....]¶

convex-hull vertices used by leginon to determine if a cursor position is within the square blob. Same coordinate system as centers.

Example json:¶

[{"vertices": [[600.4, 304.7], [502.5, 334.8], [532.7, 432.7], [630.5, 402.6]], "center": [566, 368], "area": 10488.9, "brightness": 194.2, "score": 0.3902},
 {"vertices": [[464.1, 568.5], [370.0, 597.5], [399.2, 692.5], [493.3, 663.5]], "center": [431, 630], "area": 9785.5, "brightness": 193.7, "score": 0.2530}]