@ -6,7 +6,7 @@
.nd2 files contain images and metadata, which can be split along multiple dimensions: time, fields of view (xy-plane), focus (z-plane), and filter channel. .nd2 files contain images and metadata, which can be split along multiple dimensions: time, fields of view (xy-plane), focus (z-plane), and filter channel.
`nd2reader` produces data in n umpy arrays, which makes it trivial to use with the image analysis packages such as `scikit-image` and `OpenCV` .
`nd2reader` produces data in N umpy arrays, which makes it trivial to use with the image analysis packages such as `scikit-image` and `OpenCV` .
### Installation ### Installation
@ -54,13 +54,11 @@ You can also get some metadata about the nd2 programatically:
### Images ### Images
Every method returns an `Image` object, which contains some metadata about the image as well as the
raw pixel data itself. Images are always a 16-bit grayscale image. The `data` attribute holds the numpy array
with the image data:
`Image` objects are just Numpy arrays with some extra metadata bolted on:
```python ```python
>>> image = nd2[20] >>> image = nd2[20]
>>> print(image.data )
>>> print(image)
array([[1894, 1949, 1941, ..., 2104, 2135, 2114], array([[1894, 1949, 1941, ..., 2104, 2135, 2114],
[1825, 1846, 1848, ..., 1994, 2149, 2064], [1825, 1846, 1848, ..., 1994, 2149, 2064],
[1909, 1820, 1821, ..., 1995, 1952, 2062], [1909, 1820, 1821, ..., 1995, 1952, 2062],
@ -68,49 +66,26 @@ array([[1894, 1949, 1941, ..., 2104, 2135, 2114],
[3487, 3512, 3594, ..., 3603, 3643, 3492], [3487, 3512, 3594, ..., 3603, 3643, 3492],
[3642, 3475, 3525, ..., 3712, 3682, 3609], [3642, 3475, 3525, ..., 3712, 3682, 3609],
[3687, 3777, 3738, ..., 3784, 3870, 4008]], dtype=uint16) [3687, 3777, 3738, ..., 3784, 3870, 4008]], dtype=uint16)
```
You can get a quick summary of image data by examining the `Image` object:
```python
>>> image
< ND2 Image >
1280x800 (HxW)
Timestamp: 1699.79478134
Field of View: 2
Channel: GFP
Z-Level: 1
```
Or you can access it programmatically:
```python
image = nd2[0]
print(image.timestamp)
print(image.field_of_view)
print(image.channel)
print(image.z_level)
>>> print(image.timestamp)
10.1241241248
>>> print(image.frame_number)
11
>>> print(image.field_of_view)
6
>>> print(image.channel)
'GFP'
>>> print(image.z_level)
0
``` ```
Often, you may want to just iterate over each image:
Often, you may want to just iterate over each image in the order they were acquired:
```python ```python
import nd2reader import nd2reader
nd2 = nd2reader.Nd2("/path/to/my_images.nd2") nd2 = nd2reader.Nd2("/path/to/my_images.nd2")
for image in nd2: for image in nd2:
do_something(image.data)
```
You can also get an image directly by indexing. Here, we look at the 38th image:
```python
>>> nd2[37]
< ND2 Image >
1280x800 (HxW)
Timestamp: 1699.79478134
Field of View: 2
Channel: GFP
Z-Level: 1
do_something(image)
``` ```
Slicing is also supported and is extremely memory efficient, as images are only read when directly accessed: Slicing is also supported and is extremely memory efficient, as images are only read when directly accessed:
@ -118,7 +93,7 @@ Slicing is also supported and is extremely memory efficient, as images are only
```python ```python
my_subset = nd2[50:433] my_subset = nd2[50:433]
for image in my_subset: for image in my_subset:
do_something(image.data )
do_something(image)
``` ```
Step sizes are also accepted: Step sizes are also accepted:
@ -126,44 +101,11 @@ Step sizes are also accepted:
```python ```python
for image in nd2[:100:2]: for image in nd2[:100:2]:
# gets every other image in the first 100 images # gets every other image in the first 100 images
do_something(image.data )
do_something(image)
for image in nd2[::-1]: for image in nd2[::-1]:
# iterate backwards over every image, if you're into that kind of thing # iterate backwards over every image, if you're into that kind of thing
do_something(image.data)
```
### Image Sets
If you have complicated hierarchical data, it may be easier to use image sets, which groups images together if they
share the same time index (not timestamp!) and field of view:
```python
import nd2reader
nd2 = nd2reader.Nd2("/path/to/my_complicated_images.nd2")
for image_set in nd2.image_sets:
# you can select images by channel
gfp_image = image_set.get("GFP")
do_something_gfp_related(gfp_image.data)
# you can also specify the z-level. this defaults to 0 if not given
out_of_focus_image = image_set.get("Bright Field", z_level=1)
do_something_out_of_focus_related(out_of_focus_image.data)
```
To get an image from an image set, you must specify a channel. It defaults to the 0th z-level, so if you have
more than one z-level you will need to specify it when using `get` :
```python
image = image_set.get("YFP")
image = image_set.get("YFP", z_level=2)
```
You can also see how many images are in your image set:
```python
>>> len(image_set)
7
do_something(image)
``` ```
### Protips ### Protips
jim
9 years ago