knossos-project / knossos

KNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity.
https://knossos.app
GNU General Public License v2.0
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Problem installing (anti virus) + intel driver bug #424

Open ashapsoncoe opened 7 years ago

ashapsoncoe commented 7 years ago

Hi, when trying to install Knossoss 5.0.1 on Windows 10, it states "setup failed 0x800700e8 - The pipe is being closed"

When I click on the log file the error lines read:

[27A4:27A8][2017-09-12T15:37:51]e000: Error 0x800700e8: Failed to wait for child to connect to pipe. [27A4:27A8][2017-09-12T15:37:51]e000: Error 0x800700e8: Failed to connect to elevated child process. [27A4:27A8][2017-09-12T15:37:51]e000: Error 0x800700e8: Failed to actually elevate. [27A4:27A8][2017-09-12T15:37:51]e000: Error 0x800700e8: Failed to elevate.

Can anyone suggest a solution? Probably something simple I haven't done before attempting to install?

Thanks

Alex

my-tien commented 7 years ago

Hi, Do you see the UAC window that asks you to give permission to install KNOSSOS? Do you have an antivirus program installed? It might be possible that it blocks KNOSSOS as a false positive.

ashapsoncoe commented 7 years ago

Thanks, disabling the antivirus allowed me to install it.

But now when I try to run the installed program I get a new error message (have attached a screenshot to this message).

Any suggestions?

Thanks for your help so far!

Alex

On 12 Sep 2017 16:15, "my-tien" notifications@github.com wrote:

Hi, Do you see the UAC window that asks you to give permission to install KNOSSOS? Do you have an antivirus program installed? It might be possible that it blocks KNOSSOS as a false positive.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/knossos-project/knossos/issues/424#issuecomment-328971290, or mute the thread https://github.com/notifications/unsubscribe-auth/AebJWrLVRzb23TYWoVQcizvWM6t16NSDks5shuYvgaJpZM4PVJts .

my-tien commented 7 years ago

I see that you answered via Email, but github seems to ignore your attachement, so we can’t see it. If you answer directly in the issue thread on github you can drag and drop your image into the message.

ashapsoncoe commented 7 years ago

capture

my-tien commented 7 years ago

Please give us the contents of the log.txt located at %localappdata%\MPIN\KNOSSOS 5.0\

ashapsoncoe commented 7 years ago

Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed [:0] Debug: cubeEdge: 128 , sCubeEdge: 3 , newTex: 512 ( 512 ) [:0] Debug: 1.1.0 Microsoft Corporation GDI Generic [:0] Debug: initializeOpenGLFunctions failed [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Debug: cubeEdge: 128 , sCubeEdge: 3 , newTex: 512 ( 512 ) [:0] Debug: 1.1.0 Microsoft Corporation GDI Generic [:0] Debug: initializeOpenGLFunctions failed [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Debug: cubeEdge: 128 , sCubeEdge: 3 , newTex: 512 ( 512 ) [:0] Debug: 1.1.0 Microsoft Corporation GDI Generic [:0] Debug: initializeOpenGLFunctions failed [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader [:0] Warning: QOpenGLShaderProgram: could not create shader program [:0] Warning: QOpenGLShader: could not create shader Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed Warning: Warning: Setting a new default format with a different version or profile after the global shared context is created may cause issues with context sharing. Debug: 1.1.0 Microsoft Corporation GDI Generic Debug: initializeOpenGLFunctions failed

my-tien commented 7 years ago

Okay, thank you. It looks like you need to update your graphics driver. At least OpenGL 1.3 is required.

ashapsoncoe commented 7 years ago

Thanks! I'll try that now

ashapsoncoe commented 7 years ago

Hi, I've checked and I've got Open GL 3.1, and the card is intel HD graphics 3000. My directX version is 12 (as I have windows 10).

Any other suggestions?

Alex

On Tue, Sep 12, 2017 at 5:58 PM, my-tien notifications@github.com wrote:

Okay, thank you. It looks like you need to update your graphics driver. At least OpenGL 1.3 is required.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/knossos-project/knossos/issues/424#issuecomment-328996443, or mute the thread https://github.com/notifications/unsubscribe-auth/AebJWlO2cOreLJb3TSQJF1a6IPh-k34gks5shv6KgaJpZM4PVJts .

my-tien commented 7 years ago

How did you check the version? 3.1 is the highest version supported by your igp, but the log reports that your current OpenGL version is 1.1.0. I suggest you try an update with an official driver from your manufacturer (not via windows update).

ashapsoncoe commented 7 years ago

Hi, thanks, I used the program open GL extensions viewer which stated that it is 3.1 (see attached pic). Thinking that this might be wrong, I ran the intel driver update programme, but this stated that my graphics drivers were up to date.

However, Open GL extensions viewer did generate a report, which did highlight some things not found - would any of these errors explain the errors reported in the original knossoss log file? :

Renderer: Intel(R) HD Graphics 3000 Vendor: Intel Memory: 1797 MB Version: 3.1.0 - Build 9.17.10.4459 Shading language version: 1.40 - Intel Build 9.17.10.4459

Max texture size: 8192 x 8192 Max vertex texture image units: 16 Max texture image units: 16 Max geometry texture units: 0 Max anisotropic filtering value: 16 Max viewport size: 8192 x 8192 Max Clip Distances: 6 Max samples: 4

GL Extensions: 129 \i0

GL_ARB_half_float_pixel GL_EXT_compiled_vertex_array GL_WIN_swap_hint GL_EXT_packed_depth_stencil GL_EXT_texture_lod_bias GL_INTEL_map_texture GL_ARB_color_buffer_float GL_ARB_texture_compression_rgtc GL_ARB_draw_instanced GL_EXT_draw_buffers2 GL_EXT_texture_shared_exponent GL_ARB_draw_elements_base_vertex GL_ARB_window_pos GL_ARB_explicit_attrib_location GL_ARB_texture_float GL_ARB_point_parameters GL_ARB_texture_compression GL_EXT_transform_feedback GL_ARB_depth_buffer_float GL_ARB_vertex_buffer_object GL_EXT_packed_float GL_ARB_pixel_buffer_object GL_ARB_fragment_program_shadow WGL_EXT_swap_control GL_ARB_shading_language_100 WGL_ARB_extensions_string GL_EXT_packed_pixels GL_EXT_blend_func_separate GL_INTEL_performance_queries GL_EXT_texture3D GL_ARB_texture_env_crossbar GL_EXT_stencil_wrap GL_ARB_transpose_matrix GL_EXT_texture_compression_s3tc GL_ARB_vertex_program GL_EXT_texture_sRGB WGL_EXT_pixel_format_packed_float WGL_EXT_swap_control_tear GL_ARB_texture_rectangle GL_ARB_depth_clamp GL_ARB_framebuffer_sRGB GL_ARB_texture_env_add GL_ARB_texture_rg WGL_EXT_extensions_string GL_ARB_half_float_vertex GL_SGIS_texture_edge_clamp GL_ARB_texture_cube_map GL_EXT_shadow_funcs GL_SGIS_texture_lod GL_EXT_texture_filter_anisotropic GL_EXT_multi_draw_arrays GL_EXT_texture_rectangle GL_ARB_vertex_array_object GL_ARB_shadow GL_ARB_vertex_array_bgra GL_ARB_compatibility GL_SGIS_generate_mipmap GL_EXT_blend_minmax WGL_ARB_pixel_format GL_ARB_point_sprite GL_ARB_depth_texture GL_ARB_copy_buffer WGL_ARB_make_current_read WGL_ARB_pixel_format_float GL_3DFX_texture_compression_FXT1 WGL_ARB_pbuffer GL_ARB_map_buffer_range GL_ARB_occlusion_query WGL_ARB_create_context GL_ARB_fragment_shader GL_ARB_draw_buffers GL_ARB_texture_border_clamp GL_EXT_clip_volume_hint GL_ARB_vertex_shader GL_EXT_fog_coord GL_ARB_fragment_program GL_EXT_framebuffer_blit GL_ATI_separate_stencil GL_ARB_texture_env_combine GL_EXT_abgr GL_EXT_bgra GL_ARB_texture_non_power_of_two GL_EXT_texture_edge_clamp GL_ARB_sync GL_ARB_texture_query_lod GL_EXT_separate_specular_color GL_EXT_framebuffer_object GL_EXT_texture_integer GL_NV_conditional_render GL_ARB_draw_buffers_blend GL_EXT_blend_color WGL_EXT_depth_float GL_EXT_gpu_program_parameters GL_ARB_timer_query GL_NV_texgen_reflection GL_EXT_blend_subtract WGL_ARB_multisample GL_EXT_secondary_color GL_EXT_texture_swizzle GL_ARB_provoking_vertex GL_NV_blend_square GL_EXT_texture_env_combine GL_EXT_draw_range_elements GL_EXT_texture_env_add GL_ARB_multisample GL_ARB_shader_objects GL_ARB_texture_env_dot3 GL_NV_primitive_restart GL_EXT_rescale_normal GL_EXT_blend_equation_separate GL_ARB_vertex_type_2_10_10_10_rev WGL_ARB_buffer_region GL_ARB_texture_buffer_object_rgb32 GL_ARB_instanced_arrays GL_IBM_texture_mirrored_repeat GL_ARB_uniform_buffer_object GL_EXT_framebuffer_multisample GL_EXT_stencil_two_side GL_ARB_sampler_objects GL_ARB_occlusion_query2 GL_ARB_framebuffer_object WGL_ARB_framebuffer_sRGB GL_ARB_multitexture GL_EXT_texture_array GL_ARB_seamless_cube_map GL_EXT_texture_snorm GL_ARB_texture_rgb10_a2ui GL_ARB_fragment_coord_conventions GL_ARB_shader_bit_encoding

Core features v3.0 (100 % - 23/23) v3.1 (100 % - 8/8) v3.2 (70 % - 7/10) v3.3 (70 % - 7/10) v4.0 (21 % - 3/14) v4.1 (0 % - 0/7) v4.2 (0 % - 0/13) v4.3 (0 % - 0/23) v4.4 (0 % - 0/10) v4.5 (0 % - 0/11) v4.6 (0 % - 0/11) vARB 2015 (0 % - 0/12) OpenGL driver version check (Current: 3.1.0 - Build 9.17.10.4459, Latest known: ): Latest version of display drivers found According the database, you are running the latest display drivers for your video card. No ICD registry entry The current OpenGL driver doesn't expose the SOFTWARE/Microsoft/Windows (NT)/CurrentVersion/OpenGLDrivers registry entry. Unable to detect the driver version, driver revision name and filename. Extension verification: GL_ARB_tessellation_shader was not found, but has the entry point glPatchParameteri
GL_EXT_provoking_vertex was not found, but has the entry point glProvokingVertexEXT
GL_EXT_cull_vertex was not found, but has the entry point glCullParameterdvEXT
GL_EXT_cull_vertex was not found, but has the entry point glCullParameterfvEXT
GL_KHR_debug was not found, but has the entry point glGetPointerv
GL_EXT_subtexture was not found, but has the entry point glTexSubImage1DEXT
GL_EXT_subtexture was not found, but has the entry point glTexSubImage2DEXT
GL_EXT_subtexture was not found, but has the entry point glTexSubImage3DEXT
GL_ARB_blend_func_extended was not found, but has the entry point glBindFragDataLocationIndexed
GL_ARB_blend_func_extended was not found, but has the entry point glGetFragDataIndex
GL_EXT_copy_texture was not found, but has the entry point glCopyTexImage1DEXT
GL_EXT_copy_texture was not found, but has the entry point glCopyTexImage2DEXT
GL_EXT_copy_texture was not found, but has the entry point glCopyTexSubImage1DEXT
GL_EXT_copy_texture was not found, but has the entry point glCopyTexSubImage2DEXT
GL_EXT_copy_texture was not found, but has the entry point glCopyTexSubImage3DEXT
GL_ARB_imaging was not found, but has the entry point glBlendEquation
GL_ARB_geometry_shader4 was not found, but has the entry point glFramebufferTextureARB
GL_ARB_geometry_shader4 was not found, but has the entry point glFramebufferTextureFaceARB
GL_ARB_geometry_shader4 was not found, but has the entry point glFramebufferTextureLayerARB
GL_ARB_geometry_shader4 was not found, but has the entry point glProgramParameteriARB
GL_ARB_texture_buffer_object was not found, but has the entry point glTexBufferARB
GL_EXT_gpu_shader4 was not found, but has the entry point glBindFragDataLocationEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glGetFragDataLocationEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glGetUniformuivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glGetVertexAttribIivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glGetVertexAttribIuivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform1uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform1uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform2uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform2uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform3uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform3uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform4uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glUniform4uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI1iEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI1ivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI1uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI1uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI2iEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI2ivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI2uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI2uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI3iEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI3ivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI3uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI3uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4bvEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4iEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4ivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4svEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4ubvEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4uiEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4uivEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribI4usvEXT
GL_EXT_gpu_shader4 was not found, but has the entry point glVertexAttribIPointerEXT
GL_ARB_ES2_compatibility was not found, but has the entry point glClearDepthf
GL_ARB_ES2_compatibility was not found, but has the entry point glDepthRangef
GL_ARB_ES2_compatibility was not found, but has the entry point glGetShaderPrecisionFormat
GL_ARB_ES2_compatibility was not found, but has the entry point glReleaseShaderCompiler
GL_ARB_ES2_compatibility was not found, but has the entry point glShaderBinary
GL_ARB_texture_multisample was not found, but has the entry point glGetMultisamplefv
GL_ARB_texture_multisample was not found, but has the entry point glSampleMaski
GL_ARB_texture_multisample was not found, but has the entry point glTexImage2DMultisample
GL_ARB_texture_multisample was not found, but has the entry point glTexImage3DMultisample
GL_VERSION_1_2 was not found, but has the entry point glCopyTexSubImage3D
GL_VERSION_1_2 was not found, but has the entry point glDrawRangeElements
GL_VERSION_1_2 was not found, but has the entry point glTexImage3D
GL_VERSION_1_2 was not found, but has the entry point glTexSubImage3D
GL_VERSION_1_3 was not found, but has the entry point glActiveTexture
GL_VERSION_1_3 was not found, but has the entry point glClientActiveTexture
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexImage1D
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexImage2D
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexImage3D
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexSubImage1D
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexSubImage2D
GL_VERSION_1_3 was not found, but has the entry point glCompressedTexSubImage3D
GL_VERSION_1_3 was not found, but has the entry point glGetCompressedTexImage
GL_VERSION_1_3 was not found, but has the entry point glLoadTransposeMatrixd
GL_VERSION_1_3 was not found, but has the entry point glLoadTransposeMatrixf
GL_VERSION_1_3 was not found, but has the entry point glMultTransposeMatrixd
GL_VERSION_1_3 was not found, but has the entry point glMultTransposeMatrixf
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1d
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1dv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1f
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1fv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1i
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1iv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1s
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord1sv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2d
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2dv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2f
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2fv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2i
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2iv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2s
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord2sv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3d
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3dv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3f
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3fv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3i
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3iv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3s
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord3sv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4d
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4dv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4f
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4fv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4i
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4iv
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4s
GL_VERSION_1_3 was not found, but has the entry point glMultiTexCoord4sv
GL_VERSION_1_3 was not found, but has the entry point glSampleCoverage
GL_VERSION_1_4 was not found, but has the entry point glBlendColor
GL_VERSION_1_4 was not found, but has the entry point glBlendEquation
GL_VERSION_1_4 was not found, but has the entry point glBlendFuncSeparate
GL_VERSION_1_4 was not found, but has the entry point glFogCoordPointer
GL_VERSION_1_4 was not found, but has the entry point glFogCoordd
GL_VERSION_1_4 was not found, but has the entry point glFogCoorddv
GL_VERSION_1_4 was not found, but has the entry point glFogCoordf
GL_VERSION_1_4 was not found, but has the entry point glFogCoordfv
GL_VERSION_1_4 was not found, but has the entry point glMultiDrawArrays
GL_VERSION_1_4 was not found, but has the entry point glMultiDrawElements
GL_VERSION_1_4 was not found, but has the entry point glPointParameterf
GL_VERSION_1_4 was not found, but has the entry point glPointParameterfv
GL_VERSION_1_4 was not found, but has the entry point glPointParameteri
GL_VERSION_1_4 was not found, but has the entry point glPointParameteriv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3b
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3bv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3d
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3dv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3f
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3fv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3i
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3iv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3s
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3sv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3ub
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3ubv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3ui
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3uiv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3us
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColor3usv
GL_VERSION_1_4 was not found, but has the entry point glSecondaryColorPointer
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2d
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2dv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2f
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2fv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2i
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2iv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2s
GL_VERSION_1_4 was not found, but has the entry point glWindowPos2sv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3d
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3dv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3f
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3fv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3i
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3iv
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3s
GL_VERSION_1_4 was not found, but has the entry point glWindowPos3sv
GL_VERSION_1_5 was not found, but has the entry point glBeginQuery
GL_VERSION_1_5 was not found, but has the entry point glBindBuffer
GL_VERSION_1_5 was not found, but has the entry point glBufferData
GL_VERSION_1_5 was not found, but has the entry point glBufferSubData
GL_VERSION_1_5 was not found, but has the entry point glDeleteBuffers
GL_VERSION_1_5 was not found, but has the entry point glDeleteQueries
GL_VERSION_1_5 was not found, but has the entry point glEndQuery
GL_VERSION_1_5 was not found, but has the entry point glGenBuffers
GL_VERSION_1_5 was not found, but has the entry point glGenQueries
GL_VERSION_1_5 was not found, but has the entry point glGetBufferParameteriv
GL_VERSION_1_5 was not found, but has the entry point glGetBufferPointerv
GL_VERSION_1_5 was not found, but has the entry point glGetBufferSubData
GL_VERSION_1_5 was not found, but has the entry point glGetQueryObjectiv
GL_VERSION_1_5 was not found, but has the entry point glGetQueryObjectuiv
GL_VERSION_1_5 was not found, but has the entry point glGetQueryiv
GL_VERSION_1_5 was not found, but has the entry point glIsBuffer
GL_VERSION_1_5 was not found, but has the entry point glIsQuery
GL_VERSION_1_5 was not found, but has the entry point glMapBuffer
GL_VERSION_1_5 was not found, but has the entry point glUnmapBuffer
GL_VERSION_2_0 was not found, but has the entry point glAttachShader
GL_VERSION_2_0 was not found, but has the entry point glBindAttribLocation
GL_VERSION_2_0 was not found, but has the entry point glBlendEquationSeparate
GL_VERSION_2_0 was not found, but has the entry point glCompileShader
GL_VERSION_2_0 was not found, but has the entry point glCreateProgram
GL_VERSION_2_0 was not found, but has the entry point glCreateShader
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capture

my-tien commented 7 years ago

I am not sure what causes the missing extensions. Maybe your old installation is messed up somehow, did you try removing and reinstalling graphics drivers?

ashapsoncoe commented 7 years ago

Hi, no I haven't attempted to change or update any graphics drivers since I got the laptop. Are you suggesting removing and reinstalling my graphics driver(s) as a solution?

Can we at least be certain that the missing OpenGL extensions are the cause of the failure to load Knossos?

Thanks for all your advice and apologies for my ignorance!

Alex

On Wed, Sep 13, 2017 at 12:25 PM, my-tien notifications@github.com wrote:

I am not sure what causes the missing extensions. Maybe your old installation is messed up somehow, did you try removing and reinstalling graphics drivers?

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Optiligence commented 7 years ago

The »Forward Context 3.1« is not of relevance, we want the non-forward context as selected in the attached screenshot. What KNOSSOS seems to get is the »GDI Generic« one at the beginning which shouldn’t take precedence. Yes, we suggest reinstalling the up-to-date graphics driver. image

ashapsoncoe commented 7 years ago

Hi, so the non-forward context also shows Open GL version 3.1 (see screenshot attached), and my generic one is 1.1. So it seems as though the problem is as you say that Knossos is taking the generic one over the Intel 3000 with Open GL 3.1.

Is there any way to make KNOSSOS give precedence to the non-generic one?

Thanks again.

capture

Optiligence commented 7 years ago

Did you try starting it without your antivirus, because that was also a problem for the installer?

Optiligence commented 7 years ago

KNOSSOS uses Window’s »Primary Display Driver« which should be set to your Intel driver. Applications refrain from explicitly allowing to change this for some 15 years or so now since you usually want your »Primary Display Driver«. There are programs to override this on an application basis, but that shouldn’t be necessary.

ashapsoncoe commented 7 years ago

Hi, sorry for the delayed reply. I have uninstalled and re-installed the latest Intel driver, and knossos still has the same problem where it thinks that I have open GL1.1.

I suppose the next step is to check that my Intel Open GL 3.1 driver is Windows 'Primary Display Driver' - could anyone tell me how to look for this?

Many thanks

Alex

On Wed, Sep 13, 2017 at 5:44 PM, Norbert Pfeiler notifications@github.com wrote:

KNOSSOS uses the Window’s »Primary Display Driver« which should be set to your Intel driver. Applications refrain from explicitly allowing to change this for some 15 years or so now since you usually want your »Primary Display Driver«. There are programs to override this on an application basis, but that shouldn’t be necessary.

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Optiligence commented 7 years ago

You can check what dxdiag presents as your »Main Driver« for each display. Antivirus… some folder in your %PATH% which contains another opengl32.dll

ashapsoncoe commented 7 years ago

Hi - thanks for the suggestions:

I've tried running Knossos with all antivirus switched off and it stops working in the same way.

My current primary driver is in the screenshot below - when I google igd10umd64.dll, I find that "igd10umd64.dll is part of Intel Graphics Accelerator Drivers for Windows 8(R)" - I am running windows 10, so is it possible that my Main driver is selected to be the wrong one? I.e. does igd10umd64.dll correspond to openGL 1.1, rather than Open GL 3.1?

capture

Optiligence commented 7 years ago

You CPU/GPU is officially unsupported on Windows 10. There is however a Microsoft provided driver which you have installed (9.17.10.4459). And this driver seems to be buggy in regards to OpenGL. You can try the file linked in this comment https://github.com/LWJGL/lwjgl/issues/119#issuecomment-317855127 and read a bit in the thread for more insight.

ashapsoncoe commented 7 years ago

Thanks I will have a read through that link and try the file.

In the meantime, I have searched all of my Computer for the file 'opengl32.dll' - and found the following results (in screenshot, attached). I don't suppose it is a problem having multiple copies in different places? I'm not sure which of these are in my PATH, or how to find this out?

capture

Optiligence commented 7 years ago

With what i read in the linked issue discussion I would discard PATH or any other configuration related issues now, it’s that the driver is just buggy.

ashapsoncoe commented 7 years ago

Dear all, many thanks! Running the patch from that thread seems to have fixed the problem, and Knossos now loads!

I'm not entirely sure what that patch did (fixed the buggy driver? Kept it buggy but made it less of a problem for Knossoss?) But it seems to have worked.

Incidentally, are there any major advantages of Knossos over TrakEM2/CATMAID for skeletal tracing with annotation of synaptic details?

Many thanks again for all of your help

Alex

On Mon, Sep 18, 2017 at 1:52 PM, Norbert Pfeiler notifications@github.com wrote:

With what i read in the linked issue discussion I would discard PATH or any other configuration related issues now, it’s that the driver is just buggy.

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my-tien commented 7 years ago

Regarding your question about synapse annotation, we can’t say much about the other tools. As far as I can see, CATMAID and TrackEM2 are both capable of annotating synapses. CATMAID is browser-based, you would need to set-up a server with it.

We use a tree structure to annotate the pre-synapse, post-synapse and the cleft. In the release notes for version 5 you can find an explanation, on how it’s done: https://github.com/knossos-project/knossos/releases/tag/v5.0

ashapsoncoe commented 7 years ago

Hi, thanks, I was actually trying to make synapses within Knossos using the ctrl+shift+C function, but when I do that nothing happens - the last node I placed is not labelled as 'pre-synapse', and the next node I place is just a continuation of the tree. My version of knossos is 5.0.1 if that makes a difference?

Alex

On Tue, Sep 19, 2017 at 9:37 AM, my-tien notifications@github.com wrote:

Regarding your question about synapse annotation, we can’t say much about the other tools. As far as I can see, CATMAID and TrackEM2 are both capable of annotating synapses. CATMAID is browser-based, you would need to set-up a server with it.

We use a tree structure to annotate the pre-synapse, post-synapse and the cleft. In the release notes for version 5 you can find an explanation, on how it’s done: https://github.com/knossos-project/knossos/releases/tag/ v5.0

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my-tien commented 7 years ago

It’s admittedly not at all obvious, but you need to activate “Tracing Advanced” work mode (upper left dropdown menu) for this feature. The „Tracing“ work mode is meant for simpler tracings that consist of only a single connected tree.

my-tien commented 7 years ago

Also, the shortcuts in the release notes are not correct.

  1. Shift+C after the pre-synapse node
  2. Annotate cleft
  3. C to end cleft

Next node placed is marked as the post-synapse.

ashapsoncoe commented 7 years ago

Thanks for the clarification - that works well.

One thing I'd quite like to do for each synapse is to measure the volume and signal intensity of the pre- and post-synaptic densities - this would give an objective way of determining how symmetrical (pre- vs post-synaptic intensity) each synapse is, and whether it is therefore likely to be an inhibitory or excitatory synapse.

I'm not sure there is currently a way of doing this within Knossos? I suppose I could use another application to measure the volume and intensity of any pre/post synaptic densities, and then store these data in the comment or properties section of each pre- and post-synaptic node?

my-tien commented 7 years ago

That is right, you would obtain the intensity values externally and add them to the properties of the respective node. At the moment properties can only be added by writing them into the annotation.xml inside a .k.zip file. Here is an example file.

After loading that into KNOSSOS, you can go to “Preferences > Nodes > Property Highlighting” to visualize the synapse intensities by node radius scaling.

my-tien commented 6 years ago

Hi, just to follow up: I hope everything works as expected now. Were you able to integrate KNOSSOS into your workflow? :)

ashapsoncoe commented 6 years ago

Hi, thanks for the follow-up. I am actually still collecting my data (4nm x 4nm x 30nm) serial EM slices, and was just trying to get to grips with Knossos to hit the ground running when my data is available. But still aim to use it because it seems to be the best tool for skeletal tracing.

Would there be any chance of adding a feature to measure pre/post-synaptic densities (i.e. with an integrated tool rather than an external application) into future versions of knossos?

Thanks

Alex

On Wed, Oct 4, 2017 at 11:41 AM, my-tien notifications@github.com wrote:

Hi, just to follow up: I hope everything works as expected now. Were you able to integrate KNOSSOS into your workflow? :)

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