TSFProto.proto

// This is a copy originally from: https://valelab.ucsf.edu/svn/valelabtools/TSFProto
package TSF;

option java_package = "edu.ucsf.tsf";
option java_outer_classname = "TaggedSpotsProtos";

enum FitMode {
   ONEAXIS = 0;
   TWOAXIS = 1;
   TWOAXISANDTHETA = 2;
}

enum IntensityUnits {
   COUNTS = 0;
   PHOTONS = 1;
}

enum LocationUnits {
   NM = 0;
   UM = 1;
   PIXELS = 2;
}

// If units will always be the same for all spots, then use these units tags,
message SpotList {
   // UID for the application that generated these data
   // Request a UID from nico at cmp.ucsf.edu or use 1 
   required int32 application_id = 1 [default = 1];

   optional string name = 2; // name identifying the original dataset 
   optional string filepath = 3; // path to the image data used to generate these spot data
   optional int64 uid = 4; // Unique ID, can be used by application to link to original data
   optional int32 nr_pixels_x = 5; // nr pixels in x of original data
   optional int32 nr_pixels_y = 6; // nr pixels in y of original data
   optional float pixel_size = 7; // pixel size in nanometer
   optional int64 nr_spots = 8; // number of spots in this data set
   optional int32 box_size = 17; // size (in pixels) of rectangular box used in Gaussian fitting
   optional int32 nr_channels = 18; // Nr of channels in the original data set
   optional int32 nr_frames = 19; // Nr of frames in the original data set
   optional int32 nr_slices = 20; // Nr of slices in the original data set
   optional int32 nr_pos = 21; // Nr of positions in the original data set


   // otherwise use the unit tags with each spot
   optional LocationUnits location_units = 22;
   optional IntensityUnits intensity_units = 23; // use only if different from SpotList

   // If fitmode  will always be the same for all spots, then use this fitmode
   // otherwise use the fitmode with each spot
   optional FitMode fit_mode = 24;
   optional bool is_track = 25 [default = false]; // flag indicating whether this is a sequence of spot data in consecutive time frames thought to originate from the same entity

   //repeated Spot spot = 8;

      
}
   
message Spot {
   required int32 molecule = 1; // ID for this spot
   required int32 channel = 2; // channels are 1-based
   required int32 frame = 3; // frames are 1-based
   optional int32 slice = 4; // slices are 1-based
   optional int32 pos = 5; // positions are 1-based

   // xyz coordinates of the spot in location_units  after fitting and optional correction
   optional LocationUnits location_units = 17;
   required float x = 7;
   required float y = 8;
   optional float z = 9;

   // Intensity values
   optional IntensityUnits intensity_units = 18; // use only if different from SpotList
   required float intensity = 10; // integrated spot density
   optional float background = 11; // background determined in fit
   optional float width = 12; // peak width at half height in location units
      // for asymetric peaks, calculate the width as the square root of the 
      // product of the widths of the long and short axes

   optional float a = 13; // shape of the peak: width of the long axis 
      // divided by width of the short axis
   
   optional float theta = 14; // rotation of assymetric peak, only used
      // when fitmode == TWOAXISANDTHETA


   optional int32 flag = 6; // flag to categorize spots. Implementation specific

   // Original xyz coordinates from fitting before drift or other correction correction
   optional float x_original = 101;
   optional float y_original = 102;
   optional float z_original = 103;

   // localization precision
   optional float x_precision = 104;
   optional float y_precision = 105;
   optional float z_precision = 106;
 
   // position in the original image (in pixels) used for fitting
   optional int32 x_position = 107;
   optional int32 y_position = 108;

   // These ids can be used in your own .proto derived from this one
   extensions 1500 to 2047;

}