3
$\begingroup$

EDIT: I found a workaround to this (see post below), however, the keyframe input with Still Frame Only, does not work. So I can only setup a scene of duration my number of frame in the texture. Any clue how to work around this?

Original Question:

Either this is a rendering bug, or I'm missing a critical step texture wise.

I am trying to render a Time Voxel Data set. I have my 8 bit RAW file, with time series as Still Frames.

When I select a still frame number it works just fine if I render one frame using F12, or Render (see image). So I know my texture file is good.

If I add Keyframe animation, the keyframe link works (see GIF), but then if I click on Animation to render the movie it renders all frames with the first texture and does not load the other frames (it doesn't take into account the key frame change on the Still Frame Number I guess?)

Anyone knows what I am doing wrong ?

PS: I'm using BI rendering, as voxels aren't supported in Cycles yet.

KeyFrame Works but no render

Rendering frame by frame works

$\endgroup$
  • $\begingroup$ Does it work if you don't use a keyframe and just manually set the Still frame number? $\endgroup$ – Mike Pan Feb 13 '18 at 19:58
  • $\begingroup$ It does ! that's the banging my head around part ! $\endgroup$ – Xqua Feb 13 '18 at 20:09
2
$\begingroup$

Sorry about this, I figured it out.

It was my own mistake

I checked the option Still Frame Only. To anyone reading this, MAKE SURE IT'S UNCHECKED

enter image description here

Edit: I could not find any information about this online so I made a tutorial. https://hackmd.io/s/rketOixDG

$\endgroup$
  • $\begingroup$ Can you copy said tutorial here instead. Make multiple answers if you have to. $\endgroup$ – iKlsR Feb 17 '18 at 1:26
  • $\begingroup$ I just posted it below $\endgroup$ – Xqua Feb 19 '18 at 19:32
2
$\begingroup$

Microscopy TimeLapse in Blender

This is a tutorial on how to generate a microscopy timelapse movie in blender starting from TIFF Stacks.

Concept

4D microscopy dataset are composed of a serie of 3D matrices, usually in TIFF stack. Each voxel, correspond to an intensity in 3D space. We are going to use this, and make each voxel "emmit" light in blender.

Software needed

Preparing the data

In order for blender to take a voxel dataset (3D matrix) as a texture, we need to convert our images in 8bit RAW format. To do this open FIJI, load your TIFF stack, change it's format type in Image > Type > 8-bit, then save it as RAW: File > Save As > Raw Data. (See below GIF)

Write down somewhere the dimensions of your stacks (we will need it later). For example, the stack below is: 432x622x477 (XYZ)

Multiple Time Points

If you have a timelapse, then open it with FIJI as a HyperStack, the save it as a RAW file (after 8-bit conversion). You will be able to load each frames individually in blender.

Now we are ready to open blender!

Setting up one time point in blender

At the begining there was a cube

Open up blender, and you will be presented with the default scene, a cube a lamp and a camera. That's perfect that's all we need!

Now, let's take our cube, and resize it to match the dimensions of our dataset. Select the cube (Right click on it), and press N. Type in the dimension of your dataset, BUT RESCALED BY A FACTOR 10 (except if you have a real crazy beast of a PC... and even then...).

Then came the texture

Now we need to do the actual texture mapping. In order for our cube to carry our 3D dataset, we need to give it a Voxel Data texture. Create a material, and choose Volume for its type. Set it's density to 0, making it transparent (The reason is that we can then use the values of our voxels to set the density, making our objects appear in a clear volume).

Then add a texture, and choose Voxel Data for it's type. Set all the parameters as such: - Colors - activate Ramp This is where you will adjust the transparency and colors - Voxel Data - File Format > 8 bit RAW - Source Path > Choose your RAW file generated from FIJI - Resolution > X Y Z dimension of your stack from above - check Still Frame Only - Still Frame Number > 1 - Optional: You can change the interpolation mode for better rendering results - Mapping - Coordinate > Generated - Projection > Cube - Influence - Density > Check and 1.000 - Emission > check both and 1.000 - Optional: You can play with the values, along with the transmitance, reflectance, and other texture parameters for other type of rendering

And finally came the camera

Now that our cube has a texture, we need to grab and settup our camera. In the Object Tree menu, select the camera and grab it with G. Move it outside the cube, and change the view to Active Camera using Numpad 0. Rotate and move the camera to look at the cube using the R and G keys. Once the camera is ready, you can render the cube using F12.

Alternatively, you can move around using the default 3D view, and once you have are happy with the view, you can press Ctrl + Alt + Numpad 0 to set the current view as Camera.

Setting up a movie

Now we are ready to create our first animation. We are going to use the blender Keyframes to change the time points of our dataset. Select the cube, and go to the texture tab. At the bottom of the screen set the End keyframe to the number of timepoints you have in your dataset (let's call this T, in my case 45).

Then go on the first Key, and hover the pointer over the Still Frame Number. Make sure it is at 1, and press I. (Or right click and select Insert Keyframe)

Move to the last time key, change the Still Frame Number to T, and press I again.

Rendering a movie

Now to render the movie, go to the render tab, set the resolution to your desired values (Important: the higher the resolution, the longer the rendering! If you just want to test something, use low resolutions.).

Set the output path of your animation.

Make sure the End of the movie is at T, and select the encoding. I quite like H.264, but feel free to use something else.

Finally, Click on the Animation button.

Go grab a coffee.

Results

Here are 2 example of rendering made using this, one is a single time point with 2 channel (Done with Compositing the rendering of two scenes, I'll make a tutorial about this at a later time!)

https://youtu.be/7d-0tc4HXc0 Video of 2 channels

Next is a timelapse of nuclei marked with a fluorecent reporter gene.

https://www.youtube.com/watch?v=v31WQel4eCU Video of 2 channels

Tips and tricks

Rendering in view mode

Looking at a cube to select the area of interest in a microscopy stack is not easy, and rendering images all the time makes it painful. Blender has a neat feature, that allows to render in real time.

To activate it go to the Method to display/shade object in the 3d view, and select Rendered.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.