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Sean Fitzgibbon
SlideR 🍔
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Jun 22, 2021
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Sean Fitzgibbon
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# SlideR :hamburger: : Slide Registration tools
Collection of registration tools for microscopy.
Built upon the Tensor Image Registration Library: https://git.fmrib.ox.ac.uk/ihuszar/tirl
## Dependencies
You will need to download and install miniconda to manage the python environment:
https://docs.conda.io/en/latest/miniconda.html
## Installation
First clone TIRL:
```
shell
git clone https://git.fmrib.ox.ac.uk/ihuszar/tirl.git
```
Create a virtual environment for SlideR:
```
shell
conda
env
create
-n
slider
-f
tirl/tirlenv.yml
conda activate slider
```
Install TIRL:
```
shell
cd
tirl
python setup.py
install
cd
..
```
Install SlideR:
```
shell
git clone https://git.fmrib.ox.ac.uk/seanf/slider.git
pip
install
-e
slider
```
## Usage
### Register 2D-slide to 2D-slide
You can register a 2D-slide to a 2D-slide using the
`SLIDE`
subcommand of the
`slider_app.py`
app.
```
shell
>>
slider_app.py SLIDE
-h
usage: slider_app.py SLIDE
[
-h
]
[
--out
<
dir
>]
[
--config
<config.json>]
<moving> <moving-resolution> <fixed> <fixed-resolution>
Register 2D slide to 2D slide
positional arguments:
<moving> Moving slide image
<moving-resolution> Moving image resolution
(
mm
)
<fixed> Fixed slide image
<fixed-resolution> Fixed image resolution
(
mm
)
optional arguments:
-h
,
--help
show this
help
message and
exit
--out
<
dir
>
Output directory
--config
<config.json> configuration file
```
For example:
```
shell
slider_app.py SLIDE
\
mr247MBP_c24_s20a.jp2 0.0004
\
mr247NeuN_c01_s19n.jp2 0.0004
\
--out
=
mr247_mbp_to_neun.reg
```
### Apply transform to image
Once registered, you can apply the transform to the native image using the
`APPLYXFM`
subcommand of the
`slider_app.py`
app.
```
shell
>>
slider_app.py APPLYXFM
-h
usage: slider_app.py APPLYXFM
[
-h
]
[
--inverse
]
<moving> <moving-resolution> <fixed> <fixed-resolution> <reg-moving>
<reg-fixed> <resampled-img>
Apply transform to image.
positional arguments:
<moving> Moving slide image
<moving-resolution> Moving image resolution
(
mm
)
<fixed> Fixed slide image
<fixed-resolution> Fixed image resolution
(
mm
)
<reg-moving> Moving timg from registration directory
<reg-fixed> Fixed timg from registration directory
(
e.g. fixed4_nonlinear.timg
)
<resampled-img> Name
for
resampled output image
optional arguments:
-h
,
--help
show this
help
message and
exit
--inverse
Invert the transformation chain
```
For example:
```
shell
slider_app.py APPLYXFM
\
mr247MBP_c24_s20a.jp2 0.0004
\
mr247NeuN_c01_s19n.jp2 0.0004
\
mr247_mbp_to_neun.reg/moving.timg
\
mr247_mbp_to_neun.reg/fixed4_nonlinear.timg
\
m4247_mbp_to_neun.jp2
```
Or the inverse:
```
slider_app.py APPLYXFM
\
mr247NeuN_c01_s19n.jp2 0.0004
\
mr247MBP_c24_s20a.jp2 0.0004
\
mr247_mbp_to_neun.reg/moving.timg
\
mr247_mbp_to_neun.reg/fixed4_nonlinear.timg
\
m4247_neun_to_mbp.jp2
\
--inverse
```
### Register chart to slide
You can register a Neurolucida chart file to a 2D-slide using the `CHART` subcommand of the `slider_app.py` app.
```
shell
>> slider_app.py CHART -h
usage: slider_app.py CHART [-h] [--out
<dir>
]
<chart>
<slide>
<slide-resolution>
Register charting to 2D slide
positional arguments:
<chart>
Neurolucida chart file
<slide>
Fixed slide
<slide-resolution>
Slide image resolution (mm)
optional arguments:
-h, --help show this help message and exit
--out
<dir>
Output directory
```
For example:
```
shell
slider_app.py CHART
\
mr250NeuN_c14_s03.ASC
\
mr250NeuN_c14_s03n.jp2 0.0004
\
--out=mr250_chart_to_neun.reg
```
\ No newline at end of file
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