ajay1685

/**
 * Rotate annotations or detections in QuPath.
 *
 * This creates new transformed objects that are then added to the current image hierarchy.
 *
 * Note: Tested and working with version 0.5.1.
 * Note: Watch for objects extending beyond image bounds
 * Note: Inspired from: https://gist.github.com/petebankhead/2cab4873e001ab42e03c864666284c5f
 * TODO: Use RoiTools.transformROI(roi, transform.getRotateInstance(-Math.PI/2))
 *

ajay1685

# -*- coding: utf-8 -*-
"""
Created on Fri Nov 19 14:45:08 2021

@author: Ajay Zalavadia ([email protected])_
"""
import math
import os
import glob
import logging

ajay1685

# -*- coding: utf-8 -*-
"""
This script is used for stitching the component_data.tif files generated by un-mixing workflow in inForm. This
script uses tifffile to read the metadata (Channel names & colors, spatial calibration and stage cordinates) from
input files. pyvips (libvips) is used to read the pixel data from image files and create a stitched image. The final stitched image is saved
in ome-tiff compatible format with minimal ome-xml.
Created on Wed Aug 22 15:53:08 2021
Modified on 2023-07-18: add resolution, channel names and channel colors to ome-xml. some code cleanup.
@author: Ajay Zalavadia ([email protected])
"""

ajay1685

//use BotFather to create a bot, BotFather can also provide API token for your bot
bot_token="0123456789:AaBcDeFGhxihUjCw6uiE9HED_lLuVy_dummy"

//Start a new chat and add your bot to the chat, get a chat_id for that chat 
//More information about chat id at : https://www.alphr.com/find-chat-id-telegram/
new URL("https://api.telegram.org/bot"+bot_token+"/getUpdates").text //find chat id in the response

//use the chat id found above
chat_id= "-123456789"

ajay1685

%From TrackMate export the tracks as xml 
xmlfile = 'Full path to the \Tracks.xml';
close all;
tracks = importTrackMateTracks(xmlfile);
%set track origin to zero cordinates
zeroTrackX = zeros(size(tracks{1,1}(:,2),1),size(tracks,1));
zeroTrackY = zeros(size(tracks{1,1}(:,2),1),size(tracks,1));
for i=1:1:size(tracks,1)
    zeroTrackX(:,i) = (tracks{i,1}(:,2) - (tracks{i,1}(1,2)));
    zeroTrackY(:,i) = tracks{i,1}(:,3) - (tracks{i,1}(1,3));