diff --git a/tutorials/tutorial_images/manual_transform.png b/tutorials/tutorial_images/manual_transform.png new file mode 100644 index 0000000..9eee59e Binary files /dev/null and b/tutorials/tutorial_images/manual_transform.png differ diff --git a/tutorials/tutorial_images/multi_view_reg1.png b/tutorials/tutorial_images/multi_view_reg1.png new file mode 100644 index 0000000..eab796a Binary files /dev/null and b/tutorials/tutorial_images/multi_view_reg1.png differ diff --git a/tutorials/volume_registration.md b/tutorials/volume_registration.md index 6394ecf..b75bb4d 100644 --- a/tutorials/volume_registration.md +++ b/tutorials/volume_registration.md @@ -15,7 +15,9 @@ This tutorial will show how to generate a project from multimodal volume images - you should get a Hyperstack image with 4 channels. (MitoTracker, Agglutinin, GFP-TGN46, and Hoechst) - adjust the lookup table for each channel to fit the fluorophore. (`Image > Lookup Tables`) - Currently, the MoBIE project creator only supports single channels, so we have to split the fluorescence stack into separate channels using `Image > Hyperstacks > Make Subset...` and choose the channel number. Do this with each of the 4 channels active. + (*hint:* you can use `Ctrl + 9` to get the history in ImageJ to repeat commands) --- + - create a new MoBIE project: type "mobie" in the search bar or choose `Plugins > MoBIE > Create > Create New MoBIE project...` ![createMobieProject.png](tutorial_images/createMobieProject.png) @@ -31,25 +33,40 @@ This tutorial will show how to generate a project from multimodal volume images - open the MoBIE project to see how the scaling and LUT are transferred --- -- continue the same way with the other channels, adding them to the same dataset and selection group. +- continue the same way with the other channels, adding them to the same dataset and selection group. - open the other channel views using the MoBIE UI and explore the multi-channel volume - right click into the multi-channel viewer and `Save current view` - `Save as new view`, save to `projcect` - Call the view something like "all channels" and make it part of the "FM" group - close MoBIE + --- + - open the EM data in Fiji - add the volume to MoBIE under the selection group "EM" (make new selection group) to the same dataset. The format conversion can take a couple of minutes. - open the MoBIE project and view your multichannel FM and EM together -- switch off all fluorescence channels but the Hoechst by clicking on `S` +- make all fluorescence channels but the Hoechst invisible by clicking on `S` - change contrast and transparency settings for the relevant sources (`B`) ![multiview.png](tutorial_images/multiview.png) -- right click the image "registration manual", select the EM image as we want to keep the multi-channles where they are, `Start manual transform` drag the image around. +- right click the image "registration manual", select the EM image as we want to keep the multi-channels where they are. +![img.png](tutorial_images/manual_transform.png) +- Click `Start manual transform` +- use the right mouse button to drag the image around. +- Press the `z` key to make sure rotations are around the viewing axis and use the right and left arrow keys to rotate. +- You can also use the mouse wheel to translate in `z`, and the up and down arrows to scale (dangerous). +- If necessary adjust brightness or opacity of the images using MoBIE's main window (`B`). - click `cancel manual Transform` to undo the translation and bring the image back to its original position. +- click `Accept manual Transform` to make it permanent and store the view into the project. This will only save the transformed EM source. Create a new selection group "registered". +- clear the viewer +- open the registered view an all FM channels. Check their registration by scrolling through the volume. +![img.png](tutorial_images/multi_view_reg1.png) + +--- -- use the mouse wheel to translate in `z`, make sure rotations are around the viewing axis and press the `z` key. Use the right and left arrow keys to rotate and the up and down to scale (dangerous) -- click `Accept manual Transform` to make it permanent and store the view into the project. This will only save the transformed EM source. Create a new selection group "Registration" \ No newline at end of file +- push `CTRL + y` to view the volume from the side. Make sure te mouse pointer is in the center of the feature, as it determines the viewer's rotation axis. +- repeat the manual registration of the EM volume until your registration matches in all axes. +- You could also use the mitochondria channel for refining it. \ No newline at end of file