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JaneliaSciComp / ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji
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Missing plugin for Color MIP search #2

Open mmc46 opened 6 years ago

mmc46 commented 6 years ago

I tried to use https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/tree/master/ColorDepthMIP_Generator

to generate a MIP image from an 8-bit JFRC2010 registered stack. But not long after I start the macro, I get an error: "Plugin or class not found: "8bit_Gray_Clip_plugins.Mask_Brighness_Measure" (java.lang.ClassNotFoundException: 8bit_Gray_Clip_plugins.Mask_Brighness_Measure)"

I'm using Fiji version: 2.0.0-rc-67/1.52d. Automatic Brightness adjustment ticked, DSLT version:line

Could you suggest a fix please?

Log: Choose a directory for aligned confocal files Choose a directory for Color MIP SAVE Confocal Stack; /Users/mmc46/projects/SPN/images/ MIP saving place; /Users/mmc46/projects/SPN/Color_MIP/ 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 JFRC2_SPN-split-vectashield-brain-2_02_warp_m0g80c8e1e-1x26r4.nrrd ; 0 / 1 TRY JFRC2_SPN-split-vectashield-brain-2_02_warp_m0g80c8e1e-1x26r4.nrrd ; 0 / 1 opened UseSubfolderName; 0 All channel MIP mode Channel number; 1 8bit file Maxvalue; 255 Minvalue; 0 3D stack brightness adjusted; maxvalue; 255 Inimax; 255 basicoperation done Anisotropic diffusion ON Area 1st time; 49207 mean; 255 totalpix; 472878 presize; 10.4059 % bitd; 8

HideoOtsuna commented 6 years ago

Hi Marta,

Could you send me your sample data? My email is otsunah@janelia.hhmi.org The code has been adjusted for the 12bit data. Could be some issue with the 8bit less GAL4 expressed data.

Best, Hideo