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They do not appear to work as intended. And they seem redundant anyway.

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ctrueden committed May 13, 2021
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28 changes: 14 additions & 14 deletions _pages/Diadem_Challenge_Data.md
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Expand Up @@ -12,15 +12,15 @@ If you have any comments or suggestions relating to this page, please email <em>

This data set [is described here](http://www.diademchallenge.org/olfactory_projection_fibers_readme.html). I will go through loading the example "OP\_1". Each image stack in this data set is distributed as a directory of TIFF files, one per slice. To load such a stack, go to {% include bc path='File | Import | Image Sequence'%} and select the file "1.tif". You should be shown a dialog like this:

![](/media/diadem-challenge-data-1.png "Diadem_Challenge_Data-1.png")
![](/media/diadem-challenge-data-1.png)

These default options should be fine - as you can see from the dialog it will have worked out that there are 60 image slices in that directory to be imported. If you click OK you should get a normal image stack:

![](/media/diadem-challenge-data-2.png "Diadem_Challenge_Data-2.png")
![](/media/diadem-challenge-data-2.png)

Unfortunately these TIFF files do not have the separation of these slices encoded correctly, so you should correct this manually. If you go to {% include bc path='Image | Properties'%} you will see that the pixel width, pixel height and voxel depth are all set to the same value (0.3296485). The [page with information about the data set](http://www.diademchallenge.org/olfactory_projection_fibers_readme.html) tells us that the z-separation should be three times the x and y separation, so correct the voxel depth to 3 times 0.3296485, like this:

![](/media/diadem-challenge-data-4.png "Diadem_Challenge_Data-4.png")
![](/media/diadem-challenge-data-4.png)

... and then press "OK". To save yourself from having to re-enter this calibration information, and to be able to open the stack from the "Recent Files" menu, etc. I think it's helpful to now save this stack as a single TIFF. So, I would go to "{% include bc path='File | Save As | Tiff ...'%}" and save this as OP\_1.tif in the directory above the one with individual slices.

Expand All @@ -30,7 +30,7 @@ Now start the tracing plugin by going to {% include bc path='Plugins | Segmentat

To load the SWC file with the supplied traces, click on "Load Traces / SWC File" and navigate to OP\_1.swc. When you have selected this file, you will see the following options dialog:

![](/media/diadem-challenge-data-7.png "Diadem_Challenge_Data-7.png")
![](/media/diadem-challenge-data-7.png)

The important setting here is that you should have the "Ignore calibration" option selected. You should not apply an offset or scale for this data set. When you click OK you should see that the traces are overlayed in the stack window and in the 3D viewer:

Expand Down Expand Up @@ -70,15 +70,15 @@ These offset values are taken from [the official page describing the data set](h

Now you can stitch together the images using these offsets by going to {% include bc path='Plugins | Stitching | Stitch Collection of Images'%}, browsing to the TileConfiguration.txt file you've just created and making sure you uncheck the box "compute overlap". It should look something like this:

![](/media/diadem-neocortical-layer-6-axons-1.png "Diadem_Neocortical_Layer_6_Axons-1.png")
![](/media/diadem-neocortical-layer-6-axons-1.png)

After clicking OK, this should stitch together all those stacks into one huge stack. (If there are problems, you should see details of them in the log window.)

<img src="/media/diadem-neocortical-layer-6-axons-2.png" width="750"/>

Next, you should correct the Z-calibration of the stitched stack. The data set page tells us that the z separation is 3.03 pixels, so open up {% include bc path='Image | Properties'%} and set the Voxel Depth to 3.03 times the Pixel Width:

![](/media/diadem-neocortical-layer-6-axons-3.png "Diadem_Neocortical_Layer_6_Axons-3.png")
![](/media/diadem-neocortical-layer-6-axons-3.png)

Now you should save the stitched stack, and work from that from now on. (Since the stitched stack isn't very large (156MB) one wonders why this wasn't distributed already stitched.) Save the stack with "{% include bc path='File | Save As | Tiff...'%}".

Expand All @@ -88,7 +88,7 @@ To load the SWC files, start up the tracer with {% include bc path='Plugins | Se

You might have noticed that the offsets used in stitching above had some negative Y and Z values. This means that when you load in the SWC files, you will need to apply an offset to compensate for this. (0,0,0) in the stitched image will be at (0,-14,-21) in the space of the tracings, so when you click on "Import traces / SWC file" and have chosen (for example) NC\_14.swc, you should expand the "Apply offset to SWC file co-ordinates" option and fill in these values:

![](/media/diadem-neocortical-layer-6-axons-7.png "Diadem_Neocortical_Layer_6_Axons-7.png")
![](/media/diadem-neocortical-layer-6-axons-7.png)

Then the traces should load in the correct position with those offsets:

Expand All @@ -100,7 +100,7 @@ We will go through loading in the CF\_1 image stack from the [Cerebellar Climbin

To load the files as a virtual stack, go to "{% include bc path='File | Import | Image Sequence ...'%}" and select the first file in the sequence, "01.tif". You will be presented with the import dialog, in which you should make sure that "Use virtual stack" is selected.

![](/media/diadem-cerebellar-1.png "Diadem_Cerebellar-1.png")
![](/media/diadem-cerebellar-1.png)

(Note that the number of slices in the directory (34) was automatically set.) You should now be able to browse through the stack:

Expand All @@ -118,7 +118,7 @@ It is a good idea to invert this image, since the 3D Viewer will make the low va

Before saving this out as a single 862MB stack, it is a good idea to correct the calibration of the image. The [data set web page](http://www.diademchallenge.org/cerebellar_climbing_fibers_readme.html) tells us that the separation between slices is 8.08 pixels. So, if you bring up the {% include bc path='Image | Properties'%} dialog, then you can correct the voxel depth to be 8.08 times the pixel width:

![](/media/diadem-cerebellar-5.png "Diadem_Cerebellar-5.png")
![](/media/diadem-cerebellar-5.png)

Now save this as a single TIFF stack called CF\_1.tif by going to "{% include bc path='File | Save As | Tiff ...'%}", saving it in the directory above the one with the slices, to avoid confusion.

Expand All @@ -128,11 +128,11 @@ You can now start the tracer with {% include bc path='Plugins | Segmentation | S

You may wish to adjust the transparency in the 3D viewer by selecting the image volume (left click on the image in the 3D viewer) and then going to "{% include bc path='Edit | Attributes | Change Transparency...'%}":

![](/media/diadem-cerebellar-7.png "Diadem_Cerebellar-7.png")
![](/media/diadem-cerebellar-7.png)

Now, to load the traces click on "Load Traces / SWC File" and select CF\_1.swc. You will be presented with an options box like this:

![](/media/diadem-cerebellar-7b.png "Diadem_Cerebellar-7b.png")
![](/media/diadem-cerebellar-7b.png)

Make sure that "Ignore calibration" is selected (as in that screenshot) and that there is no offset or scale set. Once loaded you should be able to see the traces as here:

Expand All @@ -144,7 +144,7 @@ The [Hippocampal CA3 Interneuron](http://www.diademchallenge.org/hippocampal_ca3

As with the other stacks, you should load the image stack using {% include bc path='Import | Image Sequence'%} and selecting the "Use virtual stack" option:

![](/media/diadem-hippocampal-ca3-interneuron-2.png "Diadem_Hippocampal_CA3_Interneuron-2.png")
![](/media/diadem-hippocampal-ca3-interneuron-2.png)

That should load in the image data:

Expand All @@ -160,7 +160,7 @@ Now convert it to 8-bit with {% include bc path='Image | Type | 8-bit'%}. (The s

Now set the voxel depth to 1.52 times the voxel width, as specified on the [data set page](http://www.diademchallenge.org/hippocampal_ca3_Interneuron_readme.html):

![](/media/diadem-hippocampal-ca3-interneuron-6.png "Diadem_Hippocampal_CA3_Interneuron-6.png")
![](/media/diadem-hippocampal-ca3-interneuron-6.png)

And then I would save this file as a TIFF stack (with {% include bc path='Save As | Tiff...'%}) so that you don't have to go through these steps again. That will need about 2GB of disk space, and will only work if your filesystem supports single files of that size.

Expand All @@ -170,7 +170,7 @@ If you now start {% include bc path='Plugins | Segmentation | Simple Neurite Tra

Then you can load the SWC files via "Load Traces / SWC file" with these options:

![](/media/diadem-hippocampal-ca3-interneuron-8.png "Diadem_Hippocampal_CA3_Interneuron-8.png")
![](/media/diadem-hippocampal-ca3-interneuron-8.png)

(I've unchecked "Replace existing paths" for this data set, since it's nice to load several SWC files into the tracer at once.) The results of loading three of the reconstructions, for example, might look like this:

Expand Down
2 changes: 1 addition & 1 deletion _pages/Help_on_Menu_Item.md
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Expand Up @@ -6,7 +6,7 @@ categories: [Help]

The convenient command {% include bc path='Help | Help on Menu Item'%} allows you to open pages on specific menu items:

![](/media/help-on-menu-item.png "Help-On-Menu-Item.png")
![](/media/help-on-menu-item.png)

The mouse cursor will change to an arrow with a question mark and the next menu item on which you click will not execute that command but open the page on this Wiki that corresponds to the selected command.

Expand Down
2 changes: 1 addition & 1 deletion _pages/Hippocampal_CA3_Interneuron.md
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Expand Up @@ -8,6 +8,6 @@ categories: [Tutorials]

(from the previous tutorial:

![](/media/hippocampal-ca3-interneuron-1.png "Hippocampal_CA3_Interneuron-1.png")
![](/media/hippocampal-ca3-interneuron-1.png)


2 changes: 1 addition & 1 deletion _pages/Launcher.md
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Expand Up @@ -56,6 +56,6 @@ If you want to test the latest UNSTABLE version, it can downloaded here:

| | | | |
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| ![ alt=Windows (32-bit) \| link=https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win32> \| x24px](/media/win.png "fig: alt=Windows (32-bit) | link=https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win32 | x24px") [ImageJ-win32.exe](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win32) | ![ alt=Windows (64-bit) \| link=<https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win64> \| x24px](/media/win.png "fig: alt=Windows (64-bit) | link=https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win64 | x24px") [ImageJ-win64.exe](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win64) | <a href="https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=macosx | x24px"><img src="/media/osx.png" width="alt=MacOS"/></a> [ImageJ-macosx](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=macosx) | ![ alt=Linux (64-bit) \| link=<https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=linux64 \| x24px](/media/tux.png "fig: alt=Linux (64-bit) | link=https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=linux64 | x24px") [ImageJ-linux64](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=linux64) |
| ![ alt=Windows (32-bit) \| link=https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win32> \| x24px](/media/win.png) [ImageJ-win32.exe](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win32) | ![ alt=Windows (64-bit) \| link=<https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win64> \| x24px](/media/win.png) [ImageJ-win64.exe](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=win64) | <a href="https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=macosx | x24px"><img src="/media/osx.png" width="alt=MacOS"/></a> [ImageJ-macosx](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=macosx) | ![ alt=Linux (64-bit) \| link=<https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=linux64 \| x24px](/media/tux.png) [ImageJ-linux64](https://maven.scijava.org/service/local/artifact/maven/redirect?r=snapshots&g=net.imagej&a=imagej-launcher&v=LATEST&e=exe&c=linux64) |

After download, rename to match the filename given above. For MacOS and Linux binaries, set the executable bit using `chmod +x`. Then replace the launcher with the new one, keeping a backup of the previous launcher in case the new one does not work.
12 changes: 6 additions & 6 deletions _pages/Mamed.md
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Expand Up @@ -19,31 +19,31 @@ categories: [Tutorials]

The Fiji packages are re-built whenever something has been uploaded to the update site, therefore it is unlikely you need to update -- unless someone pushed something new within the past few minutes. You should see a window like this:

![](/media/mamed-1.jpg "Mamed-1.jpg")
![](/media/mamed-1.jpg)

Now we need to get a special plugin called BigDataViewer. Its a bit involved, but its WORTH IT. BigDataVIewer is not yet published, but we can get it from a specific update site. Click **Advanced mode**.

![](/media/mamed-2.jpg "Mamed-2.jpg")
![](/media/mamed-2.jpg)

Now click **Manage update sites**. You get a list of default update sites.

![](/media/mamed-3.jpg "Mamed-3.jpg")
![](/media/mamed-3.jpg)

Now we need to add an update site by clicking **Add**

![](/media/pietzsch-update-site.png "Pietzsch_update_site.png")
![](/media/pietzsch-update-site.png)

In the field **URL** type *http://sites.imagej.net/Pietzsch*

*Copy and paste it, the name is rather impossible to spell ;-).*

Now after you click enter you will likely get an error message. Click **Ok** because it IS ok. Its not a feature but a bug. Finally we have to click on the check box next to the **New** update site to include it - the error message may pop up again - ignore it, click Ok.

![](/media/mamed-5.jpg "Mamed-5.jpg")
![](/media/mamed-5.jpg)

Now we are ready to proceed by clicking **close**. A new screen pops up with a lot of giberish, this is the stuff we need.

![](/media/mamed-6.jpg "Mamed-6.jpg")
![](/media/mamed-6.jpg)

Click **Apply changes** to download and install the big data viewer. You need to restart Fiji and once you do that you should have a new item in the plugins folder called **BigDataViewer**.

Expand Down
2 changes: 1 addition & 1 deletion _pages/Open_Source.md
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Expand Up @@ -4,7 +4,7 @@ title: Open Source
categories: [Development]
---

![ 64px \| left \| link=https://opensource.org/](/media/osi-symbol.png "fig: 64px | left | link=https://opensource.org/") The [ImageJ](/about) project, and related projects in the [SciJava](SciJava) software ecosystem, are open source software projects. See the [Licensing](/licensing) page for details.
![ 64px \| left \| link=https://opensource.org/](/media/osi-symbol.png) The [ImageJ](/about) project, and related projects in the [SciJava](SciJava) software ecosystem, are open source software projects. See the [Licensing](/licensing) page for details.

Everybody is welcome to [contribute](/about/contributing) with [plugins](/plugins), patches, [bug reports](/help/report-a-bug), [tutorials](/tutorials), [documentation](/learn), and artwork.

Expand Down
2 changes: 1 addition & 1 deletion _pages/about/index.md
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Expand Up @@ -180,7 +180,7 @@ The first imaging program that {% include person id='rasband' %} developed, star

Here is a timeline of software development related to ImageJ:

![](/media/timeline-history-of-imagej.png "Timeline_History_of_ImageJ.png")
![](/media/timeline-history-of-imagej.png)

## Publications

Expand Down
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