search

JaneliaSciComp / ColorMIP_Mask_Search

ColorMIP_Mask_Search plugin for Fiji
5 stars 12 forks source link

JFRC2010_3D_Mask.nrrd is not a valid choice for "mask" in line 1612 #7

Open mollykirk16 opened 3 years ago

mollykirk16 commented 3 years ago

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

HideoOtsuna commented 3 years ago

Hi,

Please open a mask color depth MIP (CDM) and the searching CDM stack in Fiji. Then run the CDM search plugin.

Thank you, Hideo

On Nov 23, 2020, at 8:32 PM, mollykirk16 notifications@github.com wrote:

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBJIL6QEHUYPYXDKLR6XKDSRMELFANCNFSM4UAHL5JA.