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\indexentry{pathflowai-preprocess command line option@\spxentry{pathflowai-preprocess command line option}!--version@\spxentry{--version}|hyperpage}{3}
\indexentry{--version@\spxentry{--version}!pathflowai-preprocess command line option@\spxentry{pathflowai-preprocess command line option}|hyperpage}{3}
\indexentry{pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}!-i, --mask\_dir \textless{}mask\_dir\textgreater{}@\spxentry{-i, --mask\_dir \textless{}mask\_dir\textgreater{}}|hyperpage}{3}
\indexentry{-i, --mask\_dir \textless{}mask\_dir\textgreater{}@\spxentry{-i, --mask\_dir \textless{}mask\_dir\textgreater{}}!pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}|hyperpage}{3}
\indexentry{pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}!-o, --output\_dir \textless{}output\_dir\textgreater{}@\spxentry{-o, --output\_dir \textless{}output\_dir\textgreater{}}|hyperpage}{3}
\indexentry{-o, --output\_dir \textless{}output\_dir\textgreater{}@\spxentry{-o, --output\_dir \textless{}output\_dir\textgreater{}}!pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}|hyperpage}{3}
\indexentry{pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}!-fr, --from\_annotations \textless{}from\_annotations\textgreater{}@\spxentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}}|hyperpage}{3}
\indexentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}@\spxentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}}!pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}|hyperpage}{3}
\indexentry{pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}!-to, --to\_annotations \textless{}to\_annotations\textgreater{}@\spxentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}}|hyperpage}{3}
\indexentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}@\spxentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}}!pathflowai-preprocess-alter\_masks command line option@\spxentry{pathflowai-preprocess-alter\_masks command line option}|hyperpage}{3}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}@\spxentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}}|hyperpage}{4}
\indexentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}@\spxentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}@\spxentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}}|hyperpage}{4}
\indexentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}@\spxentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-fr, --from\_annotations \textless{}from\_annotations\textgreater{}@\spxentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}}|hyperpage}{4}
\indexentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}@\spxentry{-fr, --from\_annotations \textless{}from\_annotations\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-to, --to\_annotations \textless{}to\_annotations\textgreater{}@\spxentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}}|hyperpage}{4}
\indexentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}@\spxentry{-to, --to\_annotations \textless{}to\_annotations\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}|hyperpage}{4}
\indexentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-rb, --remove\_background\_annotation \textless{}remove\_background\_annotation\textgreater{}@\spxentry{-rb, --remove\_background\_annotation \textless{}remove\_background\_annotation\textgreater{}}|hyperpage}{4}
\indexentry{-rb, --remove\_background\_annotation \textless{}remove\_background\_annotation\textgreater{}@\spxentry{-rb, --remove\_background\_annotation \textless{}remove\_background\_annotation\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}!-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}@\spxentry{-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}}|hyperpage}{4}
\indexentry{-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}@\spxentry{-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}}!pathflowai-preprocess-collapse\_annotations command line option@\spxentry{pathflowai-preprocess-collapse\_annotations command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-npy, --img2npy@\spxentry{-npy, --img2npy}|hyperpage}{4}
\indexentry{-npy, --img2npy@\spxentry{-npy, --img2npy}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}|hyperpage}{4}
\indexentry{-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}|hyperpage}{4}
\indexentry{-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-a, --annotations \textless{}annotations\textgreater{}@\spxentry{-a, --annotations \textless{}annotations\textgreater{}}|hyperpage}{4}
\indexentry{-a, --annotations \textless{}annotations\textgreater{}@\spxentry{-a, --annotations \textless{}annotations\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-pr, --preprocess@\spxentry{-pr, --preprocess}|hyperpage}{4}
\indexentry{-pr, --preprocess@\spxentry{-pr, --preprocess}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-pa, --patches@\spxentry{-pa, --patches}|hyperpage}{4}
\indexentry{-pa, --patches@\spxentry{-pa, --patches}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-t, --threshold \textless{}threshold\textgreater{}@\spxentry{-t, --threshold \textless{}threshold\textgreater{}}|hyperpage}{4}
\indexentry{-t, --threshold \textless{}threshold\textgreater{}@\spxentry{-t, --threshold \textless{}threshold\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}|hyperpage}{4}
\indexentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-it, --intensity\_threshold \textless{}intensity\_threshold\textgreater{}@\spxentry{-it, --intensity\_threshold \textless{}intensity\_threshold\textgreater{}}|hyperpage}{4}
\indexentry{-it, --intensity\_threshold \textless{}intensity\_threshold\textgreater{}@\spxentry{-it, --intensity\_threshold \textless{}intensity\_threshold\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-g, --generate\_finetune\_segmentation@\spxentry{-g, --generate\_finetune\_segmentation}|hyperpage}{4}
\indexentry{-g, --generate\_finetune\_segmentation@\spxentry{-g, --generate\_finetune\_segmentation}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{4}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-tc, --target\_segmentation\_class \textless{}target\_segmentation\_class\textgreater{}@\spxentry{-tc, --target\_segmentation\_class \textless{}target\_segmentation\_class\textgreater{}}|hyperpage}{5}
\indexentry{-tc, --target\_segmentation\_class \textless{}target\_segmentation\_class\textgreater{}@\spxentry{-tc, --target\_segmentation\_class \textless{}target\_segmentation\_class\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-tt, --target\_threshold \textless{}target\_threshold\textgreater{}@\spxentry{-tt, --target\_threshold \textless{}target\_threshold\textgreater{}}|hyperpage}{5}
\indexentry{-tt, --target\_threshold \textless{}target\_threshold\textgreater{}@\spxentry{-tt, --target\_threshold \textless{}target\_threshold\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-odb, --out\_db \textless{}out\_db\textgreater{}@\spxentry{-odb, --out\_db \textless{}out\_db\textgreater{}}|hyperpage}{5}
\indexentry{-odb, --out\_db \textless{}out\_db\textgreater{}@\spxentry{-odb, --out\_db \textless{}out\_db\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-am, --adjust\_mask@\spxentry{-am, --adjust\_mask}|hyperpage}{5}
\indexentry{-am, --adjust\_mask@\spxentry{-am, --adjust\_mask}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}@\spxentry{-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}}|hyperpage}{5}
\indexentry{-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}@\spxentry{-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}!-bp, --basic\_preprocess@\spxentry{-bp, --basic\_preprocess}|hyperpage}{5}
\indexentry{-bp, --basic\_preprocess@\spxentry{-bp, --basic\_preprocess}!pathflowai-preprocess-preprocess\_pipeline command line option@\spxentry{pathflowai-preprocess-preprocess\_pipeline command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}!-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}@\spxentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}}|hyperpage}{5}
\indexentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}@\spxentry{-i, --input\_patch\_db \textless{}input\_patch\_db\textgreater{}}!pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}!-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}@\spxentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}}|hyperpage}{5}
\indexentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}@\spxentry{-o, --output\_patch\_db \textless{}output\_patch\_db\textgreater{}}!pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}!-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}|hyperpage}{5}
\indexentry{-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}!pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}|hyperpage}{5}
\indexentry{pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}!-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}|hyperpage}{5}
\indexentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}!pathflowai-preprocess-remove\_basename\_from\_db command line option@\spxentry{pathflowai-preprocess-remove\_basename\_from\_db command line option}|hyperpage}{5}
\indexentry{pathflowai-visualize command line option@\spxentry{pathflowai-visualize command line option}!--version@\spxentry{--version}|hyperpage}{7}
\indexentry{--version@\spxentry{--version}!pathflowai-visualize command line option@\spxentry{pathflowai-visualize command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}|hyperpage}{7}
\indexentry{-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}|hyperpage}{7}
\indexentry{-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-p, --patch\_info\_file \textless{}patch\_info\_file\textgreater{}@\spxentry{-p, --patch\_info\_file \textless{}patch\_info\_file\textgreater{}}|hyperpage}{7}
\indexentry{-p, --patch\_info\_file \textless{}patch\_info\_file\textgreater{}@\spxentry{-p, --patch\_info\_file \textless{}patch\_info\_file\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}|hyperpage}{7}
\indexentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}@\spxentry{-ps, --patch\_size \textless{}patch\_size\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-x, --x \textless{}x\textgreater{}@\spxentry{-x, --x \textless{}x\textgreater{}}|hyperpage}{7}
\indexentry{-x, --x \textless{}x\textgreater{}@\spxentry{-x, --x \textless{}x\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-y, --y \textless{}y\textgreater{}@\spxentry{-y, --y \textless{}y\textgreater{}}|hyperpage}{7}
\indexentry{-y, --y \textless{}y\textgreater{}@\spxentry{-y, --y \textless{}y\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-o, --outputfname \textless{}outputfname\textgreater{}@\spxentry{-o, --outputfname \textless{}outputfname\textgreater{}}|hyperpage}{7}
\indexentry{-o, --outputfname \textless{}outputfname\textgreater{}@\spxentry{-o, --outputfname \textless{}outputfname\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-s, --segmentation@\spxentry{-s, --segmentation}|hyperpage}{7}
\indexentry{-s, --segmentation@\spxentry{-s, --segmentation}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}@\spxentry{-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}}|hyperpage}{7}
\indexentry{-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}@\spxentry{-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}!-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}@\spxentry{-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}}|hyperpage}{7}
\indexentry{-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}@\spxentry{-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}}!pathflowai-visualize-extract\_patch command line option@\spxentry{pathflowai-visualize-extract\_patch command line option}|hyperpage}{7}
\indexentry{pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}!-i, --img\_file \textless{}img\_file\textgreater{}@\spxentry{-i, --img\_file \textless{}img\_file\textgreater{}}|hyperpage}{8}
\indexentry{-i, --img\_file \textless{}img\_file\textgreater{}@\spxentry{-i, --img\_file \textless{}img\_file\textgreater{}}!pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}|hyperpage}{8}
\indexentry{pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}!-a, --annotation\_txt \textless{}annotation\_txt\textgreater{}@\spxentry{-a, --annotation\_txt \textless{}annotation\_txt\textgreater{}}|hyperpage}{8}
\indexentry{-a, --annotation\_txt \textless{}annotation\_txt\textgreater{}@\spxentry{-a, --annotation\_txt \textless{}annotation\_txt\textgreater{}}!pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}|hyperpage}{8}
\indexentry{pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}!-ocf, --original\_compression\_factor \textless{}original\_compression\_factor\textgreater{}@\spxentry{-ocf, --original\_compression\_factor \textless{}original\_compression\_factor\textgreater{}}|hyperpage}{8}
\indexentry{-ocf, --original\_compression\_factor \textless{}original\_compression\_factor\textgreater{}@\spxentry{-ocf, --original\_compression\_factor \textless{}original\_compression\_factor\textgreater{}}!pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}|hyperpage}{8}
\indexentry{pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}!-cf, --compression\_factor \textless{}compression\_factor\textgreater{}@\spxentry{-cf, --compression\_factor \textless{}compression\_factor\textgreater{}}|hyperpage}{8}
\indexentry{-cf, --compression\_factor \textless{}compression\_factor\textgreater{}@\spxentry{-cf, --compression\_factor \textless{}compression\_factor\textgreater{}}!pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}|hyperpage}{8}
\indexentry{pathflowai-visualize-overlay\_new\_annotations command line option@\spxentry{pathflowai-visualize-overlay\_new\_annotations command line option}!-o, --outputfilename \textless{}outputfilename\textgreater{}@\spxentry{-o, --outputfilename \textless{}outputfilename\textgreater{}}|hyperpage}{8}
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\indexentry{-i, --embeddings\_file \textless{}embeddings\_file\textgreater{}@\spxentry{-i, --embeddings\_file \textless{}embeddings\_file\textgreater{}}!pathflowai-visualize-plot\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_embeddings command line option}|hyperpage}{8}
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\indexentry{-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}@\spxentry{-ma, --max\_background\_area \textless{}max\_background\_area\textgreater{}}!pathflowai-visualize-plot\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_embeddings command line option}|hyperpage}{8}
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\indexentry{-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}!pathflowai-visualize-plot\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_embeddings command line option}|hyperpage}{8}
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\indexentry{-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}@\spxentry{-nn, --n\_neighbors \textless{}n\_neighbors\textgreater{}}!pathflowai-visualize-plot\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_embeddings command line option}|hyperpage}{8}
\indexentry{pathflowai-visualize-plot\_image command line option@\spxentry{pathflowai-visualize-plot\_image command line option}!-i, --image\_file \textless{}image\_file\textgreater{}@\spxentry{-i, --image\_file \textless{}image\_file\textgreater{}}|hyperpage}{9}
\indexentry{-i, --image\_file \textless{}image\_file\textgreater{}@\spxentry{-i, --image\_file \textless{}image\_file\textgreater{}}!pathflowai-visualize-plot\_image command line option@\spxentry{pathflowai-visualize-plot\_image command line option}|hyperpage}{9}
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\indexentry{-cf, --compression\_factor \textless{}compression\_factor\textgreater{}@\spxentry{-cf, --compression\_factor \textless{}compression\_factor\textgreater{}}!pathflowai-visualize-plot\_image command line option@\spxentry{pathflowai-visualize-plot\_image command line option}|hyperpage}{9}
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\indexentry{-o, --outputfname \textless{}outputfname\textgreater{}@\spxentry{-o, --outputfname \textless{}outputfname\textgreater{}}!pathflowai-visualize-plot\_image command line option@\spxentry{pathflowai-visualize-plot\_image command line option}|hyperpage}{9}
\indexentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}!-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}|hyperpage}{9}
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\indexentry{-b, --basename \textless{}basename\textgreater{}@\spxentry{-b, --basename \textless{}basename\textgreater{}}!pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}|hyperpage}{9}
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\indexentry{-o, --outputfilename \textless{}outputfilename\textgreater{}@\spxentry{-o, --outputfilename \textless{}outputfilename\textgreater{}}!pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}|hyperpage}{9}
\indexentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}!-mpl, --mpl\_scatter@\spxentry{-mpl, --mpl\_scatter}|hyperpage}{9}
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\indexentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}!-z, --zoom \textless{}zoom\textgreater{}@\spxentry{-z, --zoom \textless{}zoom\textgreater{}}|hyperpage}{9}
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\indexentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option@\spxentry{pathflowai-visualize-plot\_image\_umap\_embeddings command line option}!-sc, --sort\_col \textless{}sort\_col\textgreater{}@\spxentry{-sc, --sort\_col \textless{}sort\_col\textgreater{}}|hyperpage}{9}
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\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}|hyperpage}{10}
\indexentry{-i, --input\_dir \textless{}input\_dir\textgreater{}@\spxentry{-i, --input\_dir \textless{}input\_dir\textgreater{}}!pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}|hyperpage}{10}
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\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-an, --annotations@\spxentry{-an, --annotations}|hyperpage}{10}
\indexentry{-an, --annotations@\spxentry{-an, --annotations}!pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}|hyperpage}{10}
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\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-s, --segmentation@\spxentry{-s, --segmentation}|hyperpage}{10}
\indexentry{-s, --segmentation@\spxentry{-s, --segmentation}!pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}|hyperpage}{10}
\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}@\spxentry{-sc, --n\_segmentation\_classes \textless{}n\_segmentation\_classes\textgreater{}}|hyperpage}{10}
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\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}@\spxentry{-c, --custom\_segmentation \textless{}custom\_segmentation\textgreater{}}|hyperpage}{10}
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\indexentry{-ac, --annotation\_col \textless{}annotation\_col\textgreater{}@\spxentry{-ac, --annotation\_col \textless{}annotation\_col\textgreater{}}!pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}|hyperpage}{10}
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\indexentry{pathflowai-visualize-plot\_predictions command line option@\spxentry{pathflowai-visualize-plot\_predictions command line option}!-tif, --tif\_file@\spxentry{-tif, --tif\_file}|hyperpage}{10}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-m, --model\_pkl \textless{}model\_pkl\textgreater{}@\spxentry{-m, --model\_pkl \textless{}model\_pkl\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-bs, --batch\_size \textless{}batch\_size\textgreater{}@\spxentry{-bs, --batch\_size \textless{}batch\_size\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-o, --outputfilename \textless{}outputfilename\textgreater{}@\spxentry{-o, --outputfilename \textless{}outputfilename\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-mth, --method \textless{}method\textgreater{}@\spxentry{-mth, --method \textless{}method\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-ns, --n\_samples \textless{}n\_samples\textgreater{}@\spxentry{-ns, --n\_samples \textless{}n\_samples\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-visualize-shapley\_plot command line option@\spxentry{pathflowai-visualize-shapley\_plot command line option}!-p, --pred\_out \textless{}pred\_out\textgreater{}@\spxentry{-p, --pred\_out \textless{}pred\_out\textgreater{}}|hyperpage}{11}
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\indexentry{pathflowai-monitor command line option@\spxentry{pathflowai-monitor command line option}!--version@\spxentry{--version}|hyperpage}{13}
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