janeliascicomp / colormip_mask_search Goto Github PK

I am having problems generating MIPS. The error reads as follows:
Undefined variable in line 668 (called from line 563)
files = + 1;

Kindly help.
The Color MIPS Mask Search works smoothly though.

Hello,

I am running this through FIJI and my input data is eGFP labeled IHC data which has been registered to JFRC2 using the Cachero settings in CMTK. The data is located in my documents and the masks are located in the plugins folder on my hard drive. I am consistently getting this error <"JFRC2010_3D_Mask.nrrd" is not a valid choice for "mask" in line 1612>.

1612 run("Mask Median Subtraction", "mask=JFRC2010_3D_Mask.nrrd data="+stackSt+" %="+MedianSub+" subtract histogram="+histave+"");
1613 selectWindow("JFRC2010_3D_Mask.nrrd");

I would greatly appreciate your help with this if you can.

Best,

Molly Jane Kirk

I have not been able to pull updates for this package from GitHub for a long time.

error: The following untracked working tree files would be overwritten by merge:
.DS_Store
Please move or remove them before you merge.
Aborting
Updating 2b42818..3c8ab94

Hello,
I’m attempting to use the colordepthMIP generator to create colorMIP images from 8bit nrrd files. I followed the installation instructions at https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/tree/master/ColorDepthMIP_Generator. However, when I try to run the macro, I get an error message saying ‘Unrecognized command: Mask Brightness Measure” in line 1990. I tried both the Color Depth MIP batch 0315 2019 plugin and the Color Depth MIP batch 0508 2018 plugin. Do you know what might be causing this issue?

Also, which template brain do the images need to be registered to in order to use them with the ColorMIP Mask search?

Thanks for your help!

Dear Hideo,
I'm trying to set up colormip search in my computer but had some error during the plugin launch.

I'm using the latest version of Fiji. I also tried on another computer (also win 10) and it is the same problem. Could you please help me have a look? Thanks!

(Fiji Is Just) ImageJ 2.1.0/1.53c; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 101MB of 12129MB (<1%)

java.lang.NullPointerException
at Color_MIP_Mask_Search.setup(Color_MIP_Mask_Search.java:162)
at ij.plugin.filter.PlugInFilterRunner.(PlugInFilterRunner.java:48)
at ij.IJ.runUserPlugIn(IJ.java:237)
at ij.IJ.runPlugIn(IJ.java:198)
at ij.Executer.runCommand(Executer.java:150)
at ij.Executer.run(Executer.java:68)
at java.lang.Thread.run(Thread.java:748)

Best,
Neil

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!

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