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Tiago Ferreira tferr

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@tferr
tferr / BPsCentroid_1.groovy
Created June 21, 2019 15:50
# @ImageJ ij
# @LUTService lut
import java.text.DecimalFormat
import net.imglib2.display.ColorTable
import sc.fiji.snt.*
import sc.fiji.snt.io.*
import sc.fiji.snt.analysis.*
import sc.fiji.snt.annotation.*
import sc.fiji.snt.viewer.*
@tferr
tferr / Autotrace_DemoTree.py
Created June 18, 2019 17:12
# @LogService log
# @SNTService snt
# @UIService ui
"""
file: Autotrace_OP_1.py
"""
import time
from sc.fiji.snt import (Path, SNT, Tree)
@tferr
tferr / Autotrace_OP_1.py
Created June 18, 2019 16:06
# @LogService log
# @SNTService snt
# @UIService ui
"""
file: Autotrace_OP_1.py
"""
import time
from sc.fiji.snt import (Path, SNT, Tree)
@tferr
tferr / style.json
Created June 8, 2019 12:32
Dark mode theme (Mariana inspired) for ELN
{
"background-color": "#343D46",
"border-color": "#2A3138",
"page-width": 630,
"page-height": 790,
"text-color": "#F7F7F7",
"text-font-family": "Ubuntu",
"text-font-size": 11,
"margin-left": 90,
"margin-right": 30,
@tferr
tferr / DiekProblematicCells.groovy
Created March 19, 2019 15:45
SNT script that checks for the presence of an unknown ARA ID detected on manually downloaded MouseLight reconstructions.
/*
* SNT script that checks for the presence of a misterious ARA ID that
* somehow was detected on manually downloaded MouseLight reconstructions.
*/
import tracing.io.MouseLightLoader;
import org.json.*
ids = ["AA0189", "AA0360", "AA0362"]
unknowCompartmentID = 484682464
@tferr
tferr / Linux_Utils.md
Last active December 14, 2018 17:22
Linux Utils

Find Process behind UI

#https://askubuntu.com/a/138010
xprop _NET_WM_PID | sed 's/_NET_WM_PID(CARDINAL) = //' | ps `cat`

R and Rstudio

@tferr
tferr / log.log
Last active November 12, 2018 14:57
n5-viewer NPE
ferreirat@ferreirat-ws1:~/code/n5-utils$ _JAVA_OPTIONS=-Djdk.net.URLClassPath.disableClassPathURLCheck=true ./install $HOME/bin
Installing into /groups/mousebrainmicro/home/ferreirat/bin
Assuming operating system linux
Picked up _JAVA_OPTIONS: -Djdk.net.URLClassPath.disableClassPathURLCheck=true
[INFO] Scanning for projects...
Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom
Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom
Downloaded from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/22.3.0/pom-scijava-22.3.0.pom (129 kB at 239 kB/s)
Downloading from saalfeld-lab-maven-repo: https://saalfeldlab.github.io/maven/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2.pom
Downloading from imagej.public: https://maven.imagej.net/content/groups/public/org/scijava/pom-scijava-base/3.5.2/pom-scijava-base-3.5.2.
@tferr
tferr / SubfieldTool.ijm
Created June 13, 2017 16:47
Fixed size Rectangular ROI tool for IJ1
/* Subfield Tool.ijm
* IJ BAR: https://github.com/tferr/Scripts
*
* Creates a square ROI sized from on the length of a straight line
*/
var sizeRatio = 1/3;
macro "SubField Tool - C037 L0ff0 R3399" {
getCursorLoc(x, y, z, flags);
@tferr
tferr / SNT_Scripting_Example.groovy
Created June 8, 2017 19:20
Example on how to script Simple Neurite Tracer (see http://forum.imagej.net/t/macro-able-segmentation-of-filamentous-structures-axons-in-3d/5533/3?u=tferr)
//@LogService log
//@UIService ui
import ij.IJ
import ij.gui.Overlay
import features.ComputeCurvatures
import tracing.TracerThread
import tracing.Path
@tferr
tferr / GL_Convex_Hull_Plus.groovy
Created May 18, 2017 17:24
A Groovyfied version of [Gabriel Landini Convex Hull Plus](http://www.mecourse.com/landinig/software/software.html). It is a work in progress
//@ImagePlus imp
// Obtains the 2D Convex Hull ROI from a 2D binary image
// TODO: Use imagej.ops / net.imglib2.roi.geometric.Polygon
import ij.process.ImageProcessor;
import ij.gui.PolygonRoi;
def run(ImageProcessor ip) {