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* points to brainrender * update testing * refactor * refactor * badges * notes * initial inj finder commit (#11) * formatting with black * add .DS_store to gitignore * typo * update imports * update imports * deal with no obj path given * error typo * move utils too imlib * remove amap imports * optional logging to file * tidy * registration moved to imlib * keep largest object * reduce RAM usage * remove unnecessary logging args * adds lesion and track estimation and generic tools * add missing dir support for cell export * add missing dir support for cell export * reduce mem requirements * remove old code * remove old code * refactor scaling * fix failing heatmap test * update docs * ensure output directory exists * make pixel sizes mandatory * make pixel sizes mandatory (#17) * move functionality to imlib * remove hard coded smoothing * Refactor (#19) * make pixel sizes mandatory * move functionality to imlib * remove hard coded smoothing * update docs * Injectionsite (#20) * refactors code from SL to import from neuro and imlib only * moves amap_vis to neuro and removes amap and cellfinder dependencies; * format with black * amap_vis Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com> Co-authored-by: stephen <stephen.lenzi@gmail.com>
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*.~lock.* | ||
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# macOS | ||
*.DS_Store |
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# Heatmap generation | ||
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To generate a heatmap of detected cells, which shows cell distributions in a | ||
more intuitive way that showing individual cell positions: | ||
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<img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/cellfinder/master/resources/heatmap.png" alt="heatmap" width="500"/> | ||
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*Overlay on raw data and segentation from | ||
[amap](https://github.com/SainsburyWellcomeCentre) added separately* | ||
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### Usage | ||
```bash | ||
heatmap cell_classification.xml heatmap.nii raw_data registered_atlas.nii -x 2 -y 2 -z 5 | ||
``` | ||
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### Arguments | ||
Run `heatmap -h` to see all options. | ||
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#### Positional arguments | ||
* [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) | ||
classified cells file (usually `cell_classification.xml`) | ||
* Output filename. Should end with '.nii'. If the containing directory doesn't | ||
exist, it will be created. | ||
* Path to raw data (just a single channel). Used to find the shape of the | ||
raw image that the detected cell positions are defined in. | ||
* Registered atlas file from [amap](https://github.com/SainsburyWellcomeCentre) | ||
(typically run automatically in | ||
[Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder)). File | ||
is usually `registered_atlas.nii`. | ||
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#### Keyword arguments | ||
* `-x` or `--x-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the first dimension, specified in um. | ||
* `-y` or `--y-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the second dimension, specified in um. | ||
* `-z` or `--z-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the third dimension, specified in um. | ||
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#### The following options may also need to be used: | ||
* `--heatmap-bin` Heatmap bin size (um of each edge of histogram cube) | ||
* `--heatmap-smoothing` Gaussian smoothing sigma, in um. | ||
* `--no-mask-figs` Don't mask the figures (removing any areas outside the | ||
brain, from e.g. smoothing) |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,47 @@ | ||
# Heatmap generation | ||
|
||
To generate a heatmap of detected cells, which shows cell distributions in a | ||
more intuitive way that showing individual cell positions: | ||
|
||
|
||
<img src="https://raw.githubusercontent.com/SainsburyWellcomeCentre/cellfinder/master/resources/heatmap.png" alt="heatmap" width="500"/> | ||
|
||
*Overlay on raw data and segentation from | ||
[amap](https://github.com/SainsburyWellcomeCentre) added separately* | ||
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||
|
||
### Usage | ||
```bash | ||
heatmap cell_classification.xml heatmap.nii raw_data registered_atlas.nii -x 2 -y 2 -z 5 | ||
``` | ||
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||
### Arguments | ||
Run `heatmap -h` to see all options. | ||
|
||
#### Positional arguments | ||
* [Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder) | ||
classified cells file (usually `cell_classification.xml`) | ||
* Output filename. Should end with '.nii'. If the containing directory doesn't | ||
exist, it will be created. | ||
* Path to raw data (just a single channel). Used to find the shape of the | ||
raw image that the detected cell positions are defined in. | ||
* Registered atlas file from [amap](https://github.com/SainsburyWellcomeCentre) | ||
(typically run automatically in | ||
[Cellfinder](https://github.com/SainsburyWellcomeCentre/cellfinder)). File | ||
is usually `registered_atlas.nii`. | ||
|
||
|
||
#### Keyword arguments | ||
* `-x` or `--x-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the first dimension, specified in um. | ||
* `-y` or `--y-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the second dimension, specified in um. | ||
* `-z` or `--z-pixel-size` Pixel spacing of the data that the cells are | ||
defined in, in the third dimension, specified in um. | ||
|
||
|
||
#### The following options may also need to be used: | ||
* `--heatmap-bin` Heatmap bin size (um of each edge of histogram cube) | ||
* `--heatmap-smoothing` Gaussian smoothing sigma, in um. | ||
* `--no-mask-figs` Don't mask the figures (removing any areas outside the | ||
brain, from e.g. smoothing) |
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