/
mac_visualize.prj
199 lines (190 loc) · 10.8 KB
/
mac_visualize.prj
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
<configuration build-checksum="2983054967" file="/Users/ev/Documents/GitHub/CELL_ID/mac_visualize.prj" location="/Users/ev/Documents/GitHub/CELL_ID" name="mac_visualize" preferred-package-location="/Users/ev/Dropbox/Mac/Documents/GitHub/CELL_ID/mac_visualize/for_redistribution" preferred-package-type="package.type.app" target="target.ezdeploy.standalone" target-name="Application Compiler">
<param.appname>NeuroPAL_ID</param.appname>
<param.icon>${PROJECT_ROOT}/mac_visualize_resources/icon.icns</param.icon>
<param.icons>
<file>${PROJECT_ROOT}/mac_visualize_resources/icon_48.png</file>
<file>${PROJECT_ROOT}/mac_visualize_resources/icon_32.png</file>
<file>${PROJECT_ROOT}/mac_visualize_resources/icon_24.png</file>
<file>${PROJECT_ROOT}/mac_visualize_resources/icon_16.png</file>
</param.icons>
<param.version>1.8</param.version>
<param.authnamewatermark>Amin Nejatbakhsh, Eviatar Yemini, et al.</param.authnamewatermark>
<param.email />
<param.company>Columbia University</param.company>
<param.summary>NeuroPAL ID software to perform (semi-) automated identification of neurons in images of NeuroPAL strains.</param.summary>
<param.description>Please read and cite the following peer-reviewed Cell publication:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2
A free preprint is available on bioRxiv:
https://www.biorxiv.org/content/10.1101/676312v2
Citation:
Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O.
NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell. 2021 Jan 7;184(1):272- 288.e11.
https://doi.org/10.1016/j.cell.2020.12.012</param.description>
<param.screenshot>${PROJECT_ROOT}/Data/Images/NeuroPAL Software Splash Screen Small.png</param.screenshot>
<param.guid />
<param.installpath.string>/NeuroPAL_ID/</param.installpath.string>
<param.installpath.combo>option.installpath.systemwideapp</param.installpath.combo>
<param.logo>${PROJECT_ROOT}/Data/Images/NeuroPAL Software Logo.png</param.logo>
<param.install.notes>PLEASE READ THE FOLLOWING:
1. The NeuroPAL ID software is installed in /Applications/NeuroPAL_ID/application/NeuroPAL_ID.
Please add it to your dock so you can easily find it.
2. The first time it is launched, the software will be slow to open. Please be patient. Subsequently, it will open much faster.</param.install.notes>
<param.target.install.notes>In the following directions, replace MR/v910 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed.
If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following string:
MR/v910/runtime/maci64:MR/v910/sys/os/maci64:MR/v910/bin/maci64
If it is defined, set it to the following:
${DYLD_LIBRARY_PATH}:MR/v910/runtime/maci64:MR/v910/sys/os/maci64:MR/v910/bin/maci64</param.target.install.notes>
<param.intermediate>${PROJECT_ROOT}/mac_visualize/for_testing</param.intermediate>
<param.files.only>${PROJECT_ROOT}/mac_visualize/for_redistribution_files_only</param.files.only>
<param.output>${PROJECT_ROOT}/mac_visualize/for_redistribution</param.output>
<param.logdir>${PROJECT_ROOT}/mac_visualize</param.logdir>
<param.enable.clean.build>false</param.enable.clean.build>
<param.user.defined.mcr.options />
<param.target.type>subtarget.standalone</param.target.type>
<param.support.packages>
<item><package displayname="Deploy Imported Models for Deep Learning Toolbox Converter for TensorFlow Models" enabled="true" name="Deep Learning Toolbox Converter for TensorFlow Models" product="Deep Learning Toolbox"/></item>
</param.support.packages>
<param.web.mcr>false</param.web.mcr>
<param.package.mcr>true</param.package.mcr>
<param.no.mcr>false</param.no.mcr>
<param.web.mcr.name>MyAppInstaller_web</param.web.mcr.name>
<param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
<param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
<param.windows.command.prompt>false</param.windows.command.prompt>
<param.create.log>true</param.create.log>
<param.log.file>NeuroPAL_ID_log.txt</param.log.file>
<param.native.matlab>false</param.native.matlab>
<param.checkbox>false</param.checkbox>
<param.example />
<param.help.text>Syntax
-?
Input Arguments
-? print help on how to use the application
input arguments</param.help.text>
<unset>
<param.email />
<param.guid />
<param.installpath.combo />
<param.intermediate />
<param.files.only />
<param.output />
<param.logdir />
<param.enable.clean.build />
<param.target.type />
<param.no.mcr />
<param.web.mcr.name />
<param.package.mcr.name />
<param.no.mcr.name />
<param.windows.command.prompt />
<param.native.matlab />
<param.checkbox />
<param.example />
</unset>
<fileset.main>
<file>${PROJECT_ROOT}/visualize_light.mlapp</file>
</fileset.main>
<fileset.resources>
<file>${PROJECT_ROOT}/+DataHandling/PNGViewer.m</file>
<file>${PROJECT_ROOT}/Data/Documents/About.png</file>
<file>${PROJECT_ROOT}/Data/Documents/Instructions.png</file>
<file>${PROJECT_ROOT}/Data/Documents/Keyboard.png</file>
<file>${PROJECT_ROOT}/Data/Models/NN_model.mat</file>
<file>${PROJECT_ROOT}/Data/Models/atlas_xo_rgb.mat</file>
<file>${PROJECT_ROOT}/Data/Models/atlas_xo_rgbw.mat</file>
<file>${PROJECT_ROOT}/Data/Models/atlas_xx_rgb.mat</file>
<file>${PROJECT_ROOT}/Data/Models/atlas_xx_rgbw.mat</file>
<file>${PROJECT_ROOT}/Data/NeuroPAL/NeuroPAL_male_data.mat</file>
<file>${PROJECT_ROOT}/Data/NeuroPAL/male_data.mat</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfCheckJavaMemory.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfCheckJavaPath.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfGetFileExtensions.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfGetPlane.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfGetReader.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfInitLogging.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfOpen3DVolume.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfUpgradeCheck.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfopen.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bfsave.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/bioformats_package.jar</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/createMinimalOMEXMLMetadata.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/bfmatlab/private/is_octave.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/ISSUE_TEMPLATE.md</file>
<file>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/PULL_REQUEST_TEMPLATE.md</file>
<file>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/functionSignatures.json</file>
</fileset.resources>
<fileset.package>
<file>${PROJECT_ROOT}/Data/Documents/Instructions.pdf</file>
</fileset.package>
<fileset.depfun>
<file>${PROJECT_ROOT}/+DataHandling/NeuroPALImage.m</file>
<file>${PROJECT_ROOT}/+DataHandling/imreadAny.m</file>
<file>${PROJECT_ROOT}/+DataHandling/imreadCZI.m</file>
<file>${PROJECT_ROOT}/+DataHandling/imreadLif.m</file>
<file>${PROJECT_ROOT}/+DataHandling/imreadND2.m</file>
<file>${PROJECT_ROOT}/+DataHandling/imreadVlab.m</file>
<file>${PROJECT_ROOT}/+Methods/AutoDetect.m</file>
<file>${PROJECT_ROOT}/+Methods/AutoId.m</file>
<file>${PROJECT_ROOT}/+Methods/NNDetect.m</file>
<file>${PROJECT_ROOT}/+Methods/Preprocess.m</file>
<file>${PROJECT_ROOT}/+Methods/Utils.m</file>
<file>${PROJECT_ROOT}/+Methods/find_outlier.m</file>
<file>${PROJECT_ROOT}/+Methods/logsumexp.m</file>
<file>${PROJECT_ROOT}/+Methods/munkres.m</file>
<file>${PROJECT_ROOT}/+Methods/munkres_extended.m</file>
<file>${PROJECT_ROOT}/+Neurons/Hermaphrodite.m</file>
<file>${PROJECT_ROOT}/+Neurons/Image.m</file>
<file>${PROJECT_ROOT}/+Neurons/Male.m</file>
<file>${PROJECT_ROOT}/+Neurons/Neuron.m</file>
<file>${PROJECT_ROOT}/+Neurons/NeuronBirth.m</file>
<file>${PROJECT_ROOT}/+Output/Illustration.m</file>
<file>${PROJECT_ROOT}/+Output/ImageAnalysis.m</file>
<file>${PROJECT_ROOT}/+Program/GUIPreferences.m</file>
<file>${PROJECT_ROOT}/+Program/ProgramInfo.m</file>
<file>${PROJECT_ROOT}/Data/NeuroPAL/NeuroPAL_herm_data.mat</file>
<file>${PROJECT_ROOT}/Data/NeuroPAL/birth_times.mat</file>
<file>${PROJECT_ROOT}/Data/NeuroPAL/herm_data.mat</file>
<file>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/WidgetID.m</file>
<file>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/mlapptools.m</file>
</fileset.depfun>
<build-deliverables>
<file location="${PROJECT_ROOT}/mac_visualize/for_testing" name="readme.txt" optional="true">/Users/ev/Documents/GitHub/CELL_ID/mac_visualize/for_testing/readme.txt</file>
<file location="${PROJECT_ROOT}/mac_visualize/for_testing" name="splash.png" optional="false">/Users/ev/Documents/GitHub/CELL_ID/mac_visualize/for_testing/splash.png</file>
<file location="${PROJECT_ROOT}/mac_visualize/for_testing" name="NeuroPAL_ID.app" optional="false">/Users/ev/Documents/GitHub/CELL_ID/mac_visualize/for_testing/NeuroPAL_ID.app</file>
<file location="${PROJECT_ROOT}/mac_visualize/for_testing" name="run_NeuroPAL_ID.sh" optional="false">/Users/ev/Documents/GitHub/CELL_ID/mac_visualize/for_testing/run_NeuroPAL_ID.sh</file>
</build-deliverables>
<workflow />
<matlab>
<root>/Applications/MATLAB_R2021a.app</root>
<toolboxes>
<toolbox name="matlabcoder" />
<toolbox name="neuralnetwork" />
</toolboxes>
<toolbox>
<matlabcoder>
<enabled>true</enabled>
</matlabcoder>
</toolbox>
<toolbox>
<neuralnetwork>
<enabled>true</enabled>
</neuralnetwork>
</toolbox>
</matlab>
<platform>
<unix>true</unix>
<mac>true</mac>
<windows>false</windows>
<win2k>false</win2k>
<winxp>false</winxp>
<vista>false</vista>
<linux>false</linux>
<solaris>false</solaris>
<osver>10.14.6</osver>
<os32>false</os32>
<os64>true</os64>
<arch>maci64</arch>
<matlab>true</matlab>
</platform>
</configuration>
</deployment-project>