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mainwindow.ui
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<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>MainWindow</class>
<widget class="QMainWindow" name="MainWindow">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>1404</width>
<height>898</height>
</rect>
</property>
<property name="windowTitle">
<string>NeSys Utilities</string>
</property>
<widget class="QWidget" name="centralwidget">
<layout class="QVBoxLayout" name="verticalLayout_2" stretch="5,1100,1,1">
<item>
<layout class="QHBoxLayout" name="horizontalLayout_3">
<item>
<widget class="QLabel" name="lblMain_2">
<property name="font">
<font>
<family>MS Shell Dlg 2</family>
<pointsize>32</pointsize>
</font>
</property>
<property name="text">
<string>Nutil</string>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="lblMain">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Version</string>
</property>
</widget>
</item>
<item>
<widget class="QLabel" name="lblNewt">
<property name="maximumSize">
<size>
<width>199</width>
<height>64</height>
</size>
</property>
<property name="text">
<string/>
</property>
<property name="scaledContents">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QTabWidget" name="tabMain">
<property name="maximumSize">
<size>
<width>16777215</width>
<height>600</height>
</size>
</property>
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>50</weight>
<bold>false</bold>
</font>
</property>
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="tab_4">
<attribute name="title">
<string>Quick start</string>
</attribute>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0">
<widget class="QTextBrowser" name="textBrowser">
<property name="html">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:10pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" text-decoration: underline;">To start</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">1. Go to the <span style=" font-weight:600;">Operation</span> tab. </p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">2. Press <span style=" font-weight:600;">New</span> and select <span style=" font-weight:600;">Quantifier</span>, <span style=" font-weight:600;">Transform,</span> <span style=" font-weight:600;">TiffCreator</span> or<span style=" font-weight:600;"> Resize.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">3. Fill in the fields, press <span style=" font-weight:600;">Save As</span>, then <span style=" font-weight:600;">Start</span>.</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">4. The output is saved in the specified output folder. </p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" text-decoration: underline;">Operations include</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">TiffCreator</span>: conversion of images from JPEG, PNG or untiled TIFF format to the tiled TIFF format that is compatible with Transform.</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Transform</span>: 2D transformations of large tiled TIFF images, in addition to renaming, copying and downsizing. </p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Quantifier</span>: Quantification of histological labelling in the context of brain regions defined by a reference atlas. </p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Resize: </span>for resizing JPEG/PNG images with output in PNG format.</p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> <img src=":/Resources/Nutil_logo_black.png" /></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-weight:600;"><br /></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p></body></html></string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab_2">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Preferred">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>16777215</width>
<height>100000</height>
</size>
</property>
<attribute name="title">
<string>Operation</string>
</attribute>
<layout class="QHBoxLayout" name="horizontalLayout" stretch="2,8">
<item>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QGridLayout" name="gridLayout_4">
<item row="1" column="0">
<widget class="QPushButton" name="btnNew">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>New</string>
</property>
</widget>
</item>
<item row="3" column="1">
<widget class="QPushButton" name="btnClearList">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Clear list</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QPushButton" name="btnLoad_2">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Load</string>
</property>
</widget>
</item>
<item row="2" column="1">
<widget class="QPushButton" name="btnSaveAs">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Save As</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QPushButton" name="btnClearData">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Clear data</string>
</property>
</widget>
</item>
<item row="4" column="1">
<widget class="QPushButton" name="pushButton">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Quit</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QPushButton" name="btnSave">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
<property name="text">
<string>Save</string>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QListWidget" name="lstRecent">
<property name="font">
<font>
<pointsize>10</pointsize>
<weight>75</weight>
<bold>true</bold>
</font>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QScrollArea" name="scrollArea">
<property name="verticalScrollBarPolicy">
<enum>Qt::ScrollBarAlwaysOn</enum>
</property>
<property name="widgetResizable">
<bool>true</bool>
</property>
<widget class="QWidget" name="scrollAreaWidgetContents">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>1055</width>
<height>542</height>
</rect>
</property>
<widget class="QWidget" name="layoutWidget">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>976</width>
<height>513</height>
</rect>
</property>
<layout class="QGridLayout" name="gridTemplate">
<item row="0" column="1">
<spacer name="horizontalSpacer">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>40</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
</layout>
</widget>
</widget>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="tab">
<attribute name="title">
<string>Process output</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_3" rowstretch="2,1">
<item row="0" column="0">
<widget class="QTextBrowser" name="txtInfo"/>
</item>
<item row="1" column="0">
<widget class="QTextBrowser" name="txtError"/>
</item>
</layout>
</widget>
<widget class="QWidget" name="Output">
<attribute name="title">
<string>Output</string>
</attribute>
</widget>
<widget class="QWidget" name="tab_3">
<attribute name="title">
<string>About</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_2">
<item row="0" column="0">
<widget class="QTextBrowser" name="txtAbout">
<property name="font">
<font>
<family>MS Sans Serif</family>
<pointsize>10</pointsize>
<weight>50</weight>
<bold>false</bold>
</font>
</property>
<property name="focusPolicy">
<enum>Qt::NoFocus</enum>
</property>
<property name="html">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'MS Sans Serif'; font-size:10pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">About </span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Nutil aims to simplify and streamline the mechanism of pre-and-post processing 2D brain image data from mouse and rat. It is an integral part of the QUINT workflow for regional quantification of objects such as cells.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Developers </span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Nutil is developed by the Nutil team at Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo. Nutil team: Nicolaas Groeneboom, Sharon C Yates, Maja A Puchades, Jan Bjaalie.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2'; font-weight:600;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Licence</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">GNU General Public Licence version 3 </span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Funding</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Nutil was developed with support from the EBRAINS research infrastructure with funding from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA). </span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Documentation </span><span style=" font-family:'Times New Roman','serif'; font-size:12pt;"> </span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Times New Roman','serif'; font-size:12pt;">https://nutil.readthedocs.io/en/latest/ </span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Report issues and user support</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Report issues: https://github.com/Neural-Systems-at-UIO/nutil/issues</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">EBRAINS support: [email protected]</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">How to cite the tool</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Nutil: Groeneboom NE, Yates SC, Puchades MA and Bjaalie JG (2020). Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 14:37. doi: 10.3389/fninf.2020.00037</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2'; font-weight:600;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">QUINT: Yates S.C., Groeneboom N.E., Coello C., Lichtenthaler S.F., Kuhn P.H., Demuth H.U., Hartlage-Rubsamen M., Rossner S., Leergaard T.B., Kreshuk A., Puchades M.A., Bjaalie J.G. (2019). QUINT: workflow for quantification and spatial analysis of features in histological images from rodent brain. Front of Neuroinform. doi: 10.3389/fninf. 2019.00075.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">Nutil Quantifier can be used with the following reference atlases: </span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Allen Mouse Brain Atlas version 3 2015</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Allen Mouse Brain Atlas version 3 2017</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Waxholm Space Atlas of the Sprague Dawley rat v2</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Waxholm Space Atlas of the Sprague Dawley rat v3</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Waxholm Space Atlas of the Sprague Dawley rat v4</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-weight:600;">How to cite the reference atlases</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Allen Mouse Brain Atlas: </span><span style=" font-family:'Hind Siliguri','sans-serif'; font-size:14px; color:#000000; background-color:#ffffff;">© </span><span style=" font-family:'MS Shell Dlg 2';">2004 Allen Institute for Brain Science. Allen Mouse Brain Atlas. Available from: http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">Waxholm Space Atlas of the Sprague Dawley rat brain version 2, 3 and 4: RRID: SCR_017124; Papp et al., NeuroImage 97, 374-386, 2014; Papp et al., NeuroImage 105, 561-562, 2015, Kjonigsen et al., NeuroImage 108, 441-449, 2015; Osen et al., NeuroImage 199, 38-56, 2019; Kleven et al., in preparations. </span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2';"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2';">For reuse of the Waxholm Space atlas of the Sprague Dawley rat brain, see citation policy at https://www.nitrc.org/citation/?group_id=1081</span></p>
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