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mac_visualize.prj
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<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
<configuration build-checksum="3157719643" file="/Users/yemini-lab/Documents/GitHub/NeuroPAL_ID/mac_visualize.prj" location="/Users/yemini-lab/Documents/GitHub/NeuroPAL_ID" name="mac_visualize" preferred-package-location="/Users/yemini-lab/Documents/MATLAB/C:\Users\yemini-lab\Documents\GitHub\NeuroPAL_ID\mac_visualize\for_redistribution" 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>${PROJECT_ROOT}/mac_visualize_resources/icon_16.png</file>
</param.icons>
<param.version>2.1</param.version>
<param.authnamewatermark>K. Rusch, E. Yemini, A. Nejatbakhsh, et al</param.authnamewatermark>
<param.email>[email protected]</param.email>
<param.company>UMass Chan Med School, Columbia University</param.company>
<param.summary>NeuroPAL ID software to perform (semi-) automated identification of neurons in images of NeuroPAL strains.</param.summary>
<param.description>Please read and cite the following peer-reviewed Cell publication:
https://www.cell.com/cell/fulltext/S0092-8674(20)31682-2
A free preprint is available on bioRxiv:
https://www.biorxiv.org/content/10.1101/676312v2
Citation:
Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, Samuel ADT, Paninski L, Venkatachalam V, Hobert O.
NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans. Cell. 2021 Jan 7;184(1):272- 288.e11.
https://doi.org/10.1016/j.cell.2020.12.012</param.description>
<param.screenshot>${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/R2024a 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/R2024a/runtime/maca64:MR/R2024a/sys/os/maca64:MR/R2024a/bin/maca64
If it is defined, set it to the following:
${DYLD_LIBRARY_PATH}:MR/R2024a/runtime/maca64:MR/R2024a/sys/os/maca64:MR/R2024a/bin/maca64</param.target.install.notes>
<param.intermediate>${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>${PROJECT_ROOT}/mac_visualize</param.logdir>
<param.enable.clean.build>false</param.enable.clean.build>
<param.user.defined.mcr.options>-C -a '/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb'</param.user.defined.mcr.options>
<param.target.type>subtarget.standalone</param.target.type>
<param.support.packages />
<param.web.mcr>false</param.web.mcr>
<param.package.mcr>true</param.package.mcr>
<param.no.mcr>false</param.no.mcr>
<param.web.mcr.name>MyAppInstaller_web</param.web.mcr.name>
<param.package.mcr.name>MyAppInstaller_mcr</param.package.mcr.name>
<param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
<param.windows.command.prompt>false</param.windows.command.prompt>
<param.create.log>true</param.create.log>
<param.log.file>NeuroPAL_ID_log.txt</param.log.file>
<param.native.matlab>false</param.native.matlab>
<param.checkbox>false</param.checkbox>
<param.example />
<param.help.text>Syntax
-?
Input Arguments
-? print help on how to use the application
input arguments</param.help.text>
<unset>
<param.guid />
<param.installpath.combo />
<param.intermediate />
<param.files.only />
<param.output />
<param.logdir />
<param.enable.clean.build />
<param.target.type />
<param.support.packages />
<param.no.mcr />
<param.web.mcr.name />
<param.package.mcr.name />
<param.no.mcr.name />
<param.windows.command.prompt />
<param.native.matlab />
<param.checkbox />
<param.example />
</unset>
<fileset.main>
<file>${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</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>${PROJECT_ROOT}/External_Dependencies/mlapptools-develop/functionSignatures.json</file>
</fileset.resources>
<fileset.package>
<file>${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>${PROJECT_ROOT}/+Methods/MatchHist.m</file>
<file>${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>${PROJECT_ROOT}/+Methods/run_histmatch.m</file>
<file>${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>${PROJECT_ROOT}/Data/Images/ZephIR_Logo.png</file>
<file>${PROJECT_ROOT}/Data/Models/avg_hist.mat</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}/autoseg_window.mlapp</file>
<file>${PROJECT_ROOT}/channel_selector.mlapp</file>
<file>${PROJECT_ROOT}/downsample_window.mlapp</file>
<file>${PROJECT_ROOT}/guide.mat</file>
<file>${PROJECT_ROOT}/histogram_window.mlapp</file>
<file>${PROJECT_ROOT}/newtrace.mlapp</file>
<file>${PROJECT_ROOT}/nwbsave.mlapp</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+blackrock\AddNEVFile.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+blackrock\AddNSFile.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+blackrock\README.md</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+blackrock\get_channel_info.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+mworks\AddEyePos.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+mworks\README.md</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+tdt\README.md</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+tdt\TDT2NWB.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+tdt\TDTbin2mat.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+tdt\addECoG.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+contrib\+tdt\addElectrodeTable.m</file>
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<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+file\fillExport.m</file>
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<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\+space\findShapes.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\+space\getReadSpace.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\+space\segmentSelection.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\getBaseType.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\getMatType.m</file>
<file>/Users/yemini-lab/Library/Application Support/MathWorks/MATLAB Add-Ons/Collections/NeurodataWithoutBorders_matnwb/+io\getMatTypeSize.m</file>
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