ColorDepthMIP_Generator: Unrecognized command “Mask Brightness Measure”

[IsabelDAlessandro]

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!

[HideoOtsuna]

Hi,

The error means missing the plugin.

How to install plugins & lut: 1: Download https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/blob/master/ColorDepthMIP_Generator/Plugins_Color_MIP.zip & unzip. 2: Copy the whole “Plugins_Color_MIP” folder into /Fiji/plugins/ 3: Within the folder, there is “PsychedelicRainBow2.lut” file. Move the "PsychedelicRainBow2.lut” into /Fiji/luts/ 4:Restart Fiji.

Thank you, Hideo

On Jun 5, 2020, at 3:02 PM, IsabelDAlessandro notifications@github.com<mailto:notifications@github.com> wrote:

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!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/JaneliaSciComp/ColorMIP_Mask_Search/issues/3, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADBJILZILG26KMGRM6S22Q3RVE6MPANCNFSM4NU5NGHA.

[HideoOtsuna]

Sorry I forgot to answer one more question.

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

The template is JRC2018 unisex (https://www.biorxiv.org/content/10.1101/376384v1) Resolution: xyz= 0.5189161 x 0.5189161 x 1 micron https://www.dropbox.com/s/cjcslfa2daxptu8/JRC2018_UNISEX_20x_HR.nrrd?dl=0

Thank you, Hideo

On Jun 5, 2020, at 3:45 PM, Otsuna, Hideo otsunah@janelia.hhmi.org<mailto:otsunah@janelia.hhmi.org> wrote:

Hi,

The error means missing the plugin.

How to install plugins & lut: 1: Download https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/blob/master/ColorDepthMIP_Generator/Plugins_Color_MIP.zip & unzip. 2: Copy the whole “Plugins_Color_MIP” folder into /Fiji/plugins/ 3: Within the folder, there is “PsychedelicRainBow2.lut” file. Move the "PsychedelicRainBow2.lut” into /Fiji/luts/ 4:Restart Fiji.

Thank you, Hideo

On Jun 5, 2020, at 3:02 PM, IsabelDAlessandro notifications@github.com<mailto:notifications@github.com> wrote:

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!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/JaneliaSciComp/ColorMIP_Mask_Search/issues/3, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ADBJILZILG26KMGRM6S22Q3RVE6MPANCNFSM4NU5NGHA.

[rcalfredson]

Hi to both,

This problem also occurred for me, and I tried making a small edit to the file "Color_Depth_MIP_batch_0315_2019.ijm" by changing "Mask Brightness Measure" to "Mask MIP Brightness Measure".

Afterward, the script finished without errors, and the resulting image seemed accurate. Do you think this approach makes sense?

[HideoOtsuna]

Hi Robert,

Thank you for letting me know the bug. I just replaced all of "Mask Brightness Measure" to “Mask_MIP_Brightness_Measure". The plugin was older version.

We just uploaded the 40x MCFO CDM & JRC2018 unisex template for the CDM resolution into: https://www.janelia.org/open-science/color-depth-mip https://www.janelia.org/open-science/color-depth-mip All CDMs are updated to the template now.

Thank you, Hideo

On Jun 12, 2020, at 3:54 PM, Robert C. Alfredson notifications@github.com wrote:

Hi to both,

This problem also occurred for me, and I tried making a small edit to the file "Color_Depth_MIP_batch_0315_2019.ijm" by changing "Mask Brightness Measure" to "Mask MIP Brightness Measure".

Afterward, the script finished without errors, and the resulting image seemed accurate. Do you think this approach makes sense? https://user-images.githubusercontent.com/30213946/84541203-ebed8200-acc4-11ea-8891-54b610be9d5e.jpg — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/issues/3#issuecomment-643456938, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADBJIL2CZUM66QGP7RT36STRWKBWPANCNFSM4NU5NGHA.