northwestnero.blogg.se - Convert image format atlas

Convert image format atlas how to#
Convert image format atlas download#

But to make it nicer, this would require to use Big Warp to transform a list of points (defined by their coordinates) rather than an image. One thing which is not ideal is that the ROI will look like ‘broken lines’.

Convert image format atlas download#

Hi here’s one possible way of doing what you want:ġ- Download a svg image from the atlas (for instance )Ģ- Open the svg image on FIJI (it will ask for a width and height, you can keep the default parameters (700 and 512), but you can make it bigger if you wish to make it smoother).ģ- Align this image with the slice by using Big WarpĤ- Export the deformed atlas image with Big Warp (but take care, choose NEAR NEIGHBOR interpolation, that’s important!)ĥ- With the deformed atlas image, execute this groovy script ( ) -> it will transform the label image into a list ot ROI, put into the ROI Manager If it was possible to have this atlas in a standard vectorial file format, like svg (what the allen brain atlas did), or even in the form of a list of coordinates (csv for instance), things would be easier…

Second: once you have managed to get ImageJ ROIs, you need to transform them according to the deformation you defined in BigStitcher -> this part should be ok, because BigStitcher can transform a list of points (which is just what ROIs is made of).

Convert image format atlas how to#

In short : how to convert this particular file to ImageJ ROIs ? It’s doable, but it requires some work (understand the API, file format, them write some code to make a converter from this file to ImageJ ROIs)

First: this matlab file seems to have its own convention and file format (is it taken from here ? ) What it means is that it requires some work to make it ‘understandable’ by Fiji.

Hello should be possible but it’s not straightforward. Since I am a new user I cannot attacha ny file, but I will share with all of you a link to google drive folder, in which you can find the both pictures: I am working with ImageJ which run on Windows 7. The atlas picture, which has a well defined brain regions, should be transparent and just only the dashed lines should remain in order to have precise brain regions outline. Furthermore, I cannot manage on how to register properly atlas picture with my interested brain slice, in order to avoid any deformation which can compromise the outcome of cell count. I have watched tutorials on youtube and read articles as well as user manual, but still I cannot figure out how to do it. The most accurate method it will be superimpose atlas panel picture onto microscope image. I knew how to draw line with ImgaeJ but this method is not so accurate. My question(s) regards how to superimpose rat brain picture (from Paxinos Brain Atlas) onto microscope rat brain image, because I need to count cells in specific brain regions. I’m new in this forum and I’m a beginner with ImageJ. Unity (C ) Convert textures to image data, save and load on -Convert Sprite.