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JaneliaSciComp / ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji
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ColorDepthMIP_generator ran w/o error but generate nothing #4

Open shuocao818 opened 3 years ago

shuocao818 commented 3 years ago

Hello,

I installed ColorDepthMIP_Generator following the instructions. The macro 'Color Depth MIP batch 0315 2019' ran without reporting an error (see log below). However, nothing was generated after this process. My original file was a .nrrd file generated from a neuron downloaded from FlyWire EM. It was either transformed to JRC2018U template that contains 456 stacks or a JFRC2 template that contains 218 stacks. Neither of them works.

Log: Choose a directory for aligned confocal files Choose a directory for Color MIP SAVE Confocal Stack; /Users/user/Desktop/ MIP saving place; /Users/user/Desktop/ filepath; /tmp/MIP_batch.txt Desired mean; 190 JFRCpath; /Applications/Fiji.app/plugins/Plugins_Color_MIP/JFRC2010_Mask.tif VncMaskpathF; /Applications/Fiji.app/plugins/Plugins_Color_MIP/Mask_VNC_Female.tif VncMaskpathM; /Applications/Fiji.app/plugins/Plugins_Color_MIP/Mask_VNC_Male.tif JFRC3Dpath; /Applications/Fiji.app/plugins/Plugins_Color_MIP/JFRC2010_3D_Mask.nrrd done

Thank you for your help!

HideoOtsuna commented 3 years ago

Hi,

Please turn OFF “Skip MIP creation for already made in the save directory” option. This option is just recognizing file name before the file extension, not recognizing .nrrd and .tif difference.

Thank you, Hideo

On Jul 28, 2020, at 3:13 PM, shuocao818 notifications@github.com wrote:

Hello,

I installed ColorDepthMIP_Generator following the instructions. The macro 'Color Depth MIP batch 0315 2019' ran without reporting an error (see log below). However, nothing was generated after this process. My original file was a .nrrd file generated from a neuron downloaded from FlyWire EM. It was either transformed to JRC2018U template that contains 456 stacks or a JFRC2 template that contains 218 stacks. Neither of them works.

Log: Choose a directory for aligned confocal files Choose a directory for Color MIP SAVE Confocal Stack; /Users/user/Desktop/ MIP saving place; /Users/user/Desktop/ filepath; /tmp/MIP_batch.txt Desired mean; 190 JFRCpath; /Applications/Fiji.app/plugins/Plugins_Color_MIP/JFRC2010_Mask.tif VncMaskpathF; /Applications/Fiji.app/plugins/Plugins_Color_MIP/Mask_VNC_Female.tif VncMaskpathM; /Applications/Fiji.app/plugins/Plugins_Color_MIP/Mask_VNC_Male.tif JFRC3Dpath; /Applications/Fiji.app/plugins/Plugins_Color_MIP/JFRC2010_3D_Mask.nrrd done

Thank you for your help!

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shuocao818 commented 3 years ago

Thanks a lot! It is working now.