From 12e9fbfa5d3545ab6782f78a1430e95b91b2e70f Mon Sep 17 00:00:00 2001 From: daniel-rijsketic Date: Tue, 20 Aug 2024 10:59:10 -0600 Subject: [PATCH] make html --- .../ilastik_pixel_classification.doctree | Bin 16979 -> 16673 bytes .../segment/ilastik_pixel_classification.html | 4 ++-- unravel/docs/_build/html/searchindex.js | 2 +- .../segment/ilastik_pixel_classification.html | 7 ++++--- 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/unravel/docs/_build/doctrees/unravel/segment/ilastik_pixel_classification.doctree b/unravel/docs/_build/doctrees/unravel/segment/ilastik_pixel_classification.doctree index e68ae8900c50ac1ec48606770309aa25d0cd16e9..51d9d80a976810b5589223b6d9b4d70d55aa94ee 100644 GIT binary patch delta 2869 zcmb7GU2IfU5bn8UTeb_OKii*Oy1Tcf-R@7EQa~0GnahKTkkl7rPy@LTUywi$3Iq6|_7VXU@G>c1;WI!_J*K zXU=!dnfYeUUVoEK>|wUuwxi{-Q??%pSpa@2tYs&T6xBh~l5zdVC5t510YghV@-;QT zM^n4u=i=w!>5|W&$>D~Ob9b0KSWZrGOnXfWsJ3+9+T^f2kmyg!$%H&I93MywBwlEc zQ;M>(AOd4$8#nXfOn>+6{>Fxl=?A&&)r^g0J_r+~4REk%QM6Q*`2g-Qx}8^NY^COj z3tY60YT8%8RlX_OZH@9baEWlVr|rW^zcQ>OdKC?{EC+b8d<%OEcMQTGod^ z{j^r*d*M{^GHA3fv^milLn|z_*HQCf%!-7y6RjF2muXFnI;8s6lQ$h4q7GjrFStKJ zH_9ioTFs?N_}p2cw^jVj*mrma4?OGYSojUi%lsC+=eooG62rQ?PM*YJK81qLcgOUh z4??Lm{7<;&?#_0yNd{1+ld|-EHVuob+UzCPEUaGcV%H#9wWD$xUDE~IMv}eThT_8` zDUFBGi%-KpRkfuz2?sZ#k8eH0Bi?`(PlvPF0J@Q}4TB5O<)L(5Uvdz6qw&?~lFmNqn8=z z6sdTBBxRli8*2_qhY79T7IGs=I`4Ihm$K?d{2uti-^Q*&Vf~p|NOrS+vq`eM^CsCO+zXsVmYoT9 zv0RvJ_RWW6lXzs4WKymXFoR_AP>k(^b0L?+58)@uTnO#)@po`RJd^lzUz37mxkN$F zj1(+JbVS|Da6{WLL_XX5D$|^CKV#Y zqO#X4JBt`tcE6c)p|Zms5vrik#6wX|*!1$B&2ML``WO%#;S=2uWgpN2z? zM;m8s(;2NhoktG>v&bOsxFag zwQlT$?xo>y)>C2Tf9543|K2NzF>C&HXj|^~e~d13>%-4vrJtaU^iPpSrqze7FlIDh z>oUlMljvzR;QuqhnnNaBy3d511r`$+X@Uttn;#SOi!BQnbLdxE4@>NEebb8DxlcI| zQ1$Qv!p$dff!^qIC`QxvM0`-8H$O#xGC8^K7oG=%7xwEC`t#{g{bDJ8&cWNOeyP1i z5VuIs8^`IPi{bNrwGuueqAFjsDI9;;D7-uptdnC(}ZD^*VF>za>F1l>rx%U=ItONE(zn;hU z{mys3^ZT89j=W61-9u9QQV%U(bUgKP7F^FNAwL3{UJ7%v_f=PMtzKW3e_Loiw|IWr z+Ms`P(A~=|_4e?gHgAtR6!vbZnq6I6T^sO+!nM)QvokehDQwMN3M12}XEu?fBq6O` z5^6+caN&#$IFl2AQ!_GlJEwvy$uO%cUXpf74k49p97B%BNg9`7(!&`_dnE;e)6i#O zU4aESUA{I);OH|1hMiV;keQjvx}|VXUj)naeej#p1dT>hgD|?fm=*DLsMysWcUVcT z=Aq%ywdmg1QbxVN30s9?AvxlS1N6X}Tod8ob;EKU+o=O9R>;Pj+*rmG*rqX5u(b$9 zEeN0!bwR$H5AwcFUIGdJ$!&!LhNsDU>T;PTQHu_dpjV>(7#tC-^c@DmQNaD#V3tlt z3?HmDYRC^5(v|+5GC2fi3jQQF;kaoLcNK@|H8prdoo9b?BJ?`w3s;YKx}U(Quka&s z3mj%wdb&nle+c|$6FCnD%-iyBVSqTTBkb?&2)KjckVK2oiQa+&ONss)hGwJJ*8L)#Id?=J(L>^8sF>b6GdNiw||Geb8B7AQzy$ z=1FocI%r)&3|}Koj9r3OJ_9-k6;CAgQYY%p04t4oEC2GVT z7*(+1KHqTgXMy(n4%fGn(AY(VI~^u?vrR4w#COf z{SjZdqnlkZjtYq_r&1tR1>Efh^klWcf>dA=ZoBfKx%6Ff3d=G(b3L0?xN;J#W#uuh z#G;T+UJY`kZqowvq(jU+!OSIQ8b(_Sv9+JNWZNj)CfP2M?PA$BGs}{^fQKp{7bleA z0_$O<%%wetgW?)+&&q@5^0#dXNro;l;)%`ZY5;?yUS-`4cFgmp#Ja1PkU|@A0Df1lS)_4I z0(8N|pynzof|{!=u(8UdX`KYqHj}+}y zS+v9Q;Y=u6d%S2FtRmVycu16WnP{PH7FVoFG{z2;=oOrfm*`<*Ietb{Vp@z%qg3w6 zT3jV-5g4+pMTxa!Ey}H_X;Hb^;p3V^H4|!1+w1oF@TO7jeEGK5e3A^8IP2UgT=oN) zt}45?nC!Bu8LXsA1$8{9Li2@;x_AoTfH72hnk_IYyx!WX>T&W>*^xLPo*hMJ5$KWZ z7)XYIxxjuDeI{|IZ-}P{!&T^UjkQ=ecBjWm9Cw+=wu4Oh5IqwxMX!G0W7Ei#)6iB| zuMp)9TSF$wUDlF`BDbbSl<3cODTI*dmHIa{WKJ|V?`HBEl7jhIXcGR>zZv*vctz6_ zXdp-c|NzY}n*VWi|dgBW6leJ&~c@=~Tj z%H&L0x#>Xk)WQq`Ke?)Qi>_wA+w1d&y?!6p;|+y5-q#i4wt2&XKN9BLoTta_+k!Jb zegPNp@!JD@XPEE8CO+1AU${ESource code for unravel.segment.ilastik_pixel_classification
Ilastik executable files for each OS: - Linux: /usr/local/ilastik-1.3.3post3-Linux/run_ilastik.sh - Mac: /Applications/Ilastik.app/Contents/ilastik-release/run_ilastik.sh - - Windows: C:\Program Files\ilastik-1.3.3post3\run_ilastik.bat -For info on training, see: https://b-heifets.github.io/UNRAVEL/guide.html#train-an-ilastik-project +For info on training, see: + - https://b-heifets.github.io/UNRAVEL/guide.html#train-an-ilastik-project """ import argparse diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js index 240e1456..02349ed8 100644 --- a/unravel/docs/_build/html/searchindex.js +++ b/unravel/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? directories": [[0, "add-images-to-sample-directories"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[106, "cli-usage"]], "Checking changes between versions": [[2, null]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Example:": [[44, "example"]], "Get started with analysis": [[2, "get-started-with-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[30, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Installing WSL:": [[2, "installing-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[30, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[82, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Note:": [[36, "note"]], "Notes:": [[44, "notes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Output:": [[65, "output"], [65, "id3"], [65, "id5"]], "Overview and steps for voxel-wise stats": [[0, null]], "Parameters:": [[30, "parameters"], [30, "id1"], [30, "id3"], [31, "parameters"], [33, "parameters"], [36, "parameters"], [44, "parameters"], [44, "id1"], [44, "id3"], [60, "parameters"], [65, "parameters"], [65, "id1"], [65, "id4"], [87, "parameters"], [87, "id1"], [87, "id3"], [87, "id5"]], "Python usage:": [[71, "python-usage"], [106, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Returns:": [[30, "returns"], [30, "id2"], [30, "id4"], [31, "returns"], [36, "returns"], [44, "returns"], [44, "id2"], [44, "id4"], [60, "returns"], [65, "returns"], [65, "id2"], [87, "returns"], [87, "id2"], [87, "id4"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[24, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[82, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[5, "t-test-usage"]], "TL;DR": [[2, "tl-dr"]], "Terminal command cheat sheet": [[0, null]], "Todo": [[0, "id1"], [0, "id3"]], "Train an Ilastik project": [[0, null]], "Train an Ilastik project (pixel classification)": [[0, "train-an-ilastik-project-pixel-classification"]], "Tukey\u2019s test usage:": [[5, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, "un-biased-high-resolution-analysis-and-validation-of-ensembles-using-light-sheet-images"]], "UNRAVEL visualizer": [[1, "unravel-visualizer"]], "Usage": [[4, "usage"], [6, "usage"], [8, "usage"], [10, "usage"], [11, "usage"], [12, "usage"], [13, "usage"], [16, "usage"], [18, "usage"], [19, "usage"], [20, "usage"], [67, "usage"]], "Usage for Tukey\u2019s tests w/ reordering and renaming of conditions:": [[17, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"], [68, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[91, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for atlas to atlas registration:": [[72, "usage-for-atlas-to-atlas-registration"]], "Usage for forward warping atlas to tissue space:": [[108, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[108, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[64, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[64, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[64, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[89, "usage-for-renaming-directories"]], "Usage for renaming files:": [[89, "usage-for-renaming-files"]], "Usage for t-tests:": [[17, "usage-for-t-tests"], [68, "usage-for-t-tests"]], "Usage for template to template registration:": [[72, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[72, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[91, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[39, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[39, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[84, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[38, "usage-for-z-score-scaling-if-8-bit-is-needed"]], "Usage if running after cstats_validation and cstats_org_data:": [[22, "usage-if-running-after-cstats-validation-and-cstats-org-data"]], "Usage if running directly after cstats_validation:": [[22, "usage-if-running-directly-after-cstats-validation"]], "Usage if the atlas is already in native space from warp_to_native:": [[65, "usage-if-the-atlas-is-already-in-native-space-from-warp-to-native"]], "Usage if the native atlas is not available; it is not saved (faster):": [[65, "usage-if-the-native-atlas-is-not-available-it-is-not-saved-faster"]], "Usage to prep for seg_brain_mask:": [[78, "usage-to-prep-for-seg-brain-mask"]], "Usage to prep for seg_ilastik to segment full resolution immunofluorescence images:": [[78, "usage-to-prep-for-seg-ilastik-to-segment-full-resolution-immunofluorescence-images"]], "Usage to prepend sample?? to the name of files being copied:": [[84, "usage-to-prepend-sample-to-the-name-of-files-being-copied"]], "Usage to print all commands and module names:": [[83, "usage-to-print-all-commands-and-module-names"]], "Usage to print commands matching a specific string:": [[83, "usage-to-print-commands-matching-a-specific-string"]], "Usage to print common commands and descriptions:": [[83, "usage-to-print-common-commands-and-descriptions"]], "Usage to replace voxels in image with the mean intensity in the brain where mask > 0:": [[92, "usage-to-replace-voxels-in-image-with-the-mean-intensity-in-the-brain-where-mask-0"]], "Usage to zero out voxels in image where mask < 1 (e.g., to preserve signal from segmented microglia clusters):": [[92, "usage-to-zero-out-voxels-in-image-where-mask-1-e-g-to-preserve-signal-from-segmented-microglia-clusters"]], "Usage to zero out voxels in image where mask > 0 (e.g., to exclude voxels representing artifacts):": [[92, "usage-to-zero-out-voxels-in-image-where-mask-0-e-g-to-exclude-voxels-representing-artifacts"]], "Usage w/ a tissue mask (warped to atlas space):": [[102, "usage-w-a-tissue-mask-warped-to-atlas-space"]], "Usage w/ additional options:": [[99, "usage-w-additional-options"]], "Usage w/ an atlas mask (warped to atlas space):": [[102, "usage-w-an-atlas-mask-warped-to-atlas-space"]], "Usage w/ both masks for side-specific z-scoring:": [[102, "usage-w-both-masks-for-side-specific-z-scoring"]], "Usage with a custom atlas:": [[68, "usage-with-a-custom-atlas"]], "Usage:": [[3, "usage"], [14, "usage"], [15, "usage"], [21, "usage"], [23, "usage"], [24, "usage"], [26, "usage"], [34, "usage"], [35, "usage"], [36, "usage"], [37, "usage"], [38, "usage"], [40, "usage"], [41, "usage"], [42, 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"unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative module": [[8, "module-unravel.cluster_stats.effect_sizes.effect_sizes_by_sex__relative"]], "unravel.cluster_stats.fdr module": [[10, "module-unravel.cluster_stats.fdr"]], "unravel.cluster_stats.fdr_range module": [[11, "module-unravel.cluster_stats.fdr_range"]], "unravel.cluster_stats.find_incongruent_clusters module": [[12, "module-unravel.cluster_stats.find_incongruent_clusters"]], "unravel.cluster_stats.group_bilateral_data module": [[13, "module-unravel.cluster_stats.group_bilateral_data"]], "unravel.cluster_stats.index module": [[16, "module-unravel.cluster_stats.index"]], "unravel.cluster_stats.legend module": [[15, "module-unravel.cluster_stats.legend"]], "unravel.cluster_stats.mean_IF module": [[14, "module-unravel.cluster_stats.mean_IF"]], "unravel.cluster_stats.mean_IF_summary module": [[17, "module-unravel.cluster_stats.mean_IF_summary"]], "unravel.cluster_stats.org_data module": [[18, "module-unravel.cluster_stats.org_data"]], "unravel.cluster_stats.prism module": [[19, "module-unravel.cluster_stats.prism"]], "unravel.cluster_stats.recursively_mirror_rev_cluster_indices module": [[20, "module-unravel.cluster_stats.recursively_mirror_rev_cluster_indices"]], "unravel.cluster_stats.stats_table module": [[21, "module-unravel.cluster_stats.stats_table"]], "unravel.cluster_stats.summary module": [[22, "module-unravel.cluster_stats.summary"]], "unravel.cluster_stats.sunburst module": [[23, "module-unravel.cluster_stats.sunburst"]], "unravel.cluster_stats.table module": [[24, "module-unravel.cluster_stats.table"]], "unravel.cluster_stats.validation module": [[26, "module-unravel.cluster_stats.validation"]], "unravel.core package": [[32, "unravel-core-package"]], "unravel.core.argparse_utils module": [[27, "module-unravel.core.argparse_utils"]], "unravel.core.argparse_utils_rich module": [[28, "module-unravel.core.argparse_utils_rich"]], "unravel.core.config module": [[29, 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"usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"], [68, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[91, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for atlas to atlas registration:": [[72, "usage-for-atlas-to-atlas-registration"]], "Usage for forward warping atlas to tissue space:": [[108, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[108, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[64, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[64, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for printing unique intensities w/ a min cluster size > 100 voxels:": [[64, "usage-for-printing-unique-intensities-w-a-min-cluster-size-100-voxels"]], "Usage for renaming directories:": [[89, "usage-for-renaming-directories"]], "Usage for renaming files:": [[89, "usage-for-renaming-files"]], "Usage for t-tests:": [[17, "usage-for-t-tests"], [68, "usage-for-t-tests"]], "Usage for template to template registration:": [[72, "usage-for-template-to-template-registration"]], "Usage for tissue registration:": [[72, "usage-for-tissue-registration"]], "Usage for toggling all sample?? dirs to active:": [[91, "usage-for-toggling-all-sample-dirs-to-active"]], "Usage for when metadata is extractable:": [[39, "usage-for-when-metadata-is-extractable"]], "Usage for when metadata is not extractable:": [[39, "usage-for-when-metadata-is-not-extractable"]], "Usage for when sample?? is already in the name of files being copied:": [[84, "usage-for-when-sample-is-already-in-the-name-of-files-being-copied"]], "Usage for z-score scaling (if 8 bit is needed):": [[38, 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a/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html b/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html index d98633d1..b199beb2 100644 --- a/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html +++ b/unravel/docs/_build/html/unravel/segment/ilastik_pixel_classification.html @@ -517,12 +517,13 @@

Usage:#
Ilastik executable files for each OS:

  • Linux: /usr/local/ilastik-1.3.3post3-Linux/run_ilastik.sh

  • Mac: /Applications/Ilastik.app/Contents/ilastik-release/run_ilastik.sh

    • -

  • Windows: C:Program Filesilastik-1.3.3post3

    • +
+
+
For info on training, see:
-

un_ilastik.bat

-

For info on training, see: https://b-heifets.github.io/UNRAVEL/guide.html#train-an-ilastik-project