Taro Kiritani tarokiritani
tarokiritani
/ Preprocess_Stack_for_Cell_Counting.ijm
Created
April 28, 2017 09:23
imagej macro that preprocesses confocal image stack for cell counting
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| run("Bandpass Filter...", "filter_large=100 filter_small=5.1 suppress=None tolerance=5 autoscale process"); | |
| for(i=1;i<nSlices + 1;i++){ | |
| setSlice(i); | |
| getStatistics(area, mean, min, max, std, histogram); | |
| setThreshold(mean + 2 * std, 255); | |
| run("Make Binary", "slice"); | |
| } |
tarokiritani
/ Count_helper.ijm
Created
March 10, 2017 15:09
a helper imagej macro for counting objects in 3D
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| roiManager("Show All"); | |
| run("Remove Overlay"); | |
| for (i=0; i<roiManager("count"); i++){ | |
| roiManager("select",i); | |
| roiManager("Measure"); | |
| x=getResult("X"); | |
| y=getResult("Y"); | |
| z=getResult("Slice"); | |
| for (j=-14; j<14; j++){ | |
| setSlice(z+j); |
tarokiritani
/ jupyter_collapse_headings_html
Created
January 22, 2017 12:51
small script to collapse headings in jupyter notebook after converted to html
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| <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.1.1/jquery.min.js"> | |
| </script> | |
| <script> | |
| $(document).ready(function(){ | |
| var all_cells = $("div.cell"); | |
| $.each(all_cells, function( index, value ) { | |
| if ($(value).find("h1").length == 0){ | |
| $(value).hide() | |
| } else{ | |
| var bare_h1 = $(value).find("h1").text() |
tarokiritani
/ readroi.py
Created
November 6, 2015 13:33
— forked from luispedro/readroi.py
Read ImageJ's ROI files
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| # Copyright: Luis Pedro Coelho <[email protected]>, 2012 | |
| # License: MIT | |
| import numpy as np | |
| def read_roi(fileobj): | |
| ''' | |
| points = read_roi(fileobj) | |
| Read ImageJ's ROI format | |
| ''' |