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| /* | |
| Author: LESLIE SOLORZANO (do not erase name) | |
| if you make changes then add your name but | |
| don't delete mine to make it look like it's yours. | |
| */ | |
| def annotations = getAnnotationObjects() | |
| def imageData = getCurrentImageData() | |
| def name = GeneralTools.getNameWithoutExtension(imageData.getServer().getMetadata().getName()) | |
| def path = "/home/leslie/Downloads/"+name+".json" |
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| import matplotlib.pyplot as plt | |
| from matplotlib.colors import ListedColormap | |
| import pandas as pd | |
| import numpy as np | |
| import seaborn as sns | |
| def plotUMAP(indf,colx,coly,colz,color_col=None,s=5,marker=".",frac=1,linewidths=0,xlim=[-4.0, 15.0],ylim=[-4.0, 15.0],edgecolors=None): | |
| fig=plt.figure(figsize=(9,3),dpi=500) | |
| cycled = [colx,coly,colz,colx] | |
| adf=indf.sample(frac=frac) |
lesolorzanov
/ cleanobj.py
Created
March 7, 2021 12:42
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| import json | |
| import matplotlib.pyplot as plt | |
| import numpy as np | |
| class NumpyEncoder(json.JSONEncoder): | |
| """ Custom encoder for numpy data types """ | |
| def default(self, obj): | |
| if isinstance(obj, (np.int_, np.intc, np.intp, np.int8, | |
| np.int16, np.int32, np.int64, np.uint8, | |
| np.uint16, np.uint32, np.uint64)): |
lesolorzanov
/ QuPathImportAnnotations.groovy
Last active
December 9, 2020 10:25
Importig Annotation path objects after classifying outside of QuPath
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| // Title: Importig Annotation path objects after classifying outside of QuPath | |
| // Author: Leslie Solorzano | |
| // Date: 9 dec 2020 | |
| import qupath.lib.objects.PathObjects | |
| import qupath.lib.roi.ROIs | |
| import qupath.lib.regions.ImagePlane | |
| import qupath.lib.io.GsonTools | |
| import qupath.lib.geom.Point2 | |
| import qupath.lib.objects.classes.PathClass |
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| location="/home/leslie/Documents/alphaamd/" | |
| imgs=["cells2little.png"] | |
| def drawboxesat(pdx, iw, ih, q): | |
| step=1/q | |
| for x in range(iw): | |
| for y in range(ih): | |
| intensity=pdx[(x,y)][0] | |
| if intensity==0: |
lesolorzanov
/ mergiwild.ipynb
Last active
May 31, 2019 17:39
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lesolorzanov
/ iwild.html
Last active
May 27, 2019 16:49
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| <html> | |
| <head> | |
| <script src="https://d3js.org/d3.v4.min.js"></script> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/p5.js/0.8.0/p5.js"></script> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script> | |
| <script src="/home/leslie/Downloads/iWildCam_2019_iNat_Idaho.json"></script> | |
| <script src="/home/leslie/Downloads/iWildCam_2019_CCT_Bboxes.json"></script> | |
| <!-- Latest compiled and minified CSS --> | |
| <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css" |
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| var exampleapp={ | |
| starCount:0, | |
| OSDviewer: null, | |
| init: function(){ | |
| var OSDviewer = OpenSeadragon(this.OSDOptions); | |
| this.OSDviewer=OSDviewer; | |
| this.OSDsvgov=this.OSDviewer.svgOverlay(); | |
| var click_handler= function(event) { | |
| if(event.quick){ |
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| close all | |
| clear all | |
| fname ='C:\Users\Administrator\Documents\Leslie\Uppsala\registered161101\crops\b1-2-0001-1757-1887-White Top Hat.tif'; | |
| info = imfinfo(fname); | |
| num_images = numel(info); | |
| w =info.Width; | |
| h= info.Height; |
lesolorzanov
/ screens.m
Created
January 9, 2017 11:05
Enhances spots and creates gimplike screen version
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| clear all; | |
| base=5; | |
| if(base==1) | |
| b3=imread('MAX_base_1_ch3.tif'); | |
| b4=imread('MAX_base_1_ch4.tif'); | |
| b5=imread('MAX_base_1_ch5.tif'); | |
| b6=imread('MAX_base_1_ch6.tif'); | |
| finalname='b1-color.tif'; |
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