Skip to content

Commit 4909cfa

Browse files
ctruedenctrueden
committed
Make the sample image download links clearer
1 parent d6e2ffb commit 4909cfa

4 files changed

Lines changed: 30 additions & 8 deletions

File tree

‎docs/ops/doc/examples/deconvolution.rst‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,12 @@ The SciJava Ops framework currently supports the standard RL algorithm as well a
88
algorithm, which utilizes a regularization factor to limit the noise amplified by the RL algorithm :sup:`1`. Typically,
99
the RLTV algorithm returns improved axial and lateral resolution when compared to RL.
1010

11-
You can download the 3D HeLa cell nuclus dataset `here`_.
11+
You can download the 3D HeLa cell nucleus dataset here:
12+
13+
.. admonition:: Download
14+
:class: note
15+
16+
`hela_nucleus.tif`_
1217

1318
.. figure:: https://media.scijava.org/scijava-ops/1.0.0/rltv_example_1.gif
1419

@@ -145,5 +150,5 @@ SciJava Ops via Fiji's scripting engine with `script parameters`_:
145150
146151
.. _`Dey et. al, Micros Res Tech 2006`: https://pubmed.ncbi.nlm.nih.gov/16586486/
147152
.. _`Gibson & Lanni, JOSA 1992`: https://pubmed.ncbi.nlm.nih.gov/1738047/
148-
.. _`here`: https://media.scijava.org/scijava-ops/1.0.0/hela_nucleus.tif
153+
.. _`hela_nucleus.tif`: https://media.scijava.org/scijava-ops/1.0.0/hela_nucleus.tif
149154
.. _`script parameters`: https://imagej.net/scripting/parameters

‎docs/ops/doc/examples/opencv_denoise.rst‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,12 @@ a pixel of interest (*e.g.* a 5x5 patch) with patches from other pixels from the
99
patches are then averaged to eliminate gaussian noise, without the requirement of additional
1010
images for comparison.
1111

12-
The sample data for this example can be downloaded `here`_.
12+
The sample data for this example can be downloaded here:
13+
14+
.. admonition:: Download
15+
:class: note
16+
17+
`opencv_denoise_16bit.tif`_
1318

1419
.. figure:: https://media.scijava.org/scijava-ops/1.0.0/opencv_denoise_example_1.png
1520

@@ -121,4 +126,4 @@ SciJava Ops via Fiji's scripting engine with `script parameters`_:
121126

122127
.. _`script parameters`: https://imagej.net/scripting/parameters
123128
.. _`OpenCV library`: https://docs.opencv.org/4.x/d5/d69/tutorial_py_non_local_means.html
124-
.. _`here`: https://media.scijava.org/scijava-ops/1.0.0/opencv_denoise_16bit.tif
129+
.. _`opencv_denoise_16bit.tif`: https://media.scijava.org/scijava-ops/1.0.0/opencv_denoise_16bit.tif

‎docs/ops/doc/examples/saca.rst‎

Lines changed: 7 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,12 @@ can be computed easily by using the *Z*-score heatmap with the ``stats.pnorm`` O
1717
significantly colocalized. This example script takes advantage of this feature of the SACA framework and utilizes the significant pixel
1818
mask as a region of interest to compute Pearson's :sup:`4` and Li's :sup:`5` colocalization coefficients.
1919

20-
You can download the colocalization dataset `here`_.
20+
You can download the colocalization dataset here:
21+
22+
.. admonition:: Download
23+
:class: note
24+
25+
`hela_hiv_gag_ms2_mcherry.tif`_
2126

2227
.. figure:: https://media.scijava.org/scijava-ops/1.0.0/saca_input.png
2328

@@ -169,5 +174,5 @@ To apply the ``phase`` LUT and a colorbar use the following script and select th
169174
.. _`Becker and Sherer, JVI 2017`: https://pubmed.ncbi.nlm.nih.gov/28053097/
170175
.. _`Wang et. al, IEEE 2019`: https://ieeexplore.ieee.org/abstract/document/8681436
171176
.. _`Stockley et. al, Bacteriophage 2016`: https://pubmed.ncbi.nlm.nih.gov/27144089/
172-
.. _`here`: https://media.scijava.org/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry.tif
177+
.. _`hela_hiv_gag_ms2_mcherry.tif`: https://media.scijava.org/scijava-ops/1.0.0/hela_hiv_gag_ms2_mcherry.tif
173178
.. _`script parameters`: https://imagej.net/scripting/parameters

‎docs/ops/doc/examples/volume_labeling.rst‎

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,7 +21,14 @@ to accomplish this analysis goal the script utilizes SciJava Ops to:
2121
5. Measure the 3D geometry of the puncta and nuclear regions.
2222
6. Display results in two tables (puncta and nuclear).
2323

24-
To use the script in the example first download the sample dataset `here`_. Next, open Fiji, the sample image and this scipt. Click **Run** to create the script parameter GUI,
24+
To use the script in the example, first download the sample dataset:
25+
26+
.. admonition:: Download
27+
:class: note
28+
29+
`hela_hiv_vif.tif`_
30+
31+
Next, open Fiji, the sample image and this script. Click **Run** to create the script parameter GUI,
2532
where you can customize some values to your own data, such as the channel names, channel position and image calibration values.
2633

2734
.. figure:: https://media.scijava.org/scijava-ops/1.1.0/labeling_mesh_example_dialog.png
@@ -295,4 +302,4 @@ In addition to the result tables, the label imdage (also known as an *index imag
295302
ui.show("{} results table".format(ch_a_name), ab_table)
296303
ui.show("{} results table".format(ch_b_name), b_table)
297304

298-
.. _`here`: https://media.scijava.org/scijava-ops/1.0.0/hela_hiv_vif.tif
305+
.. _`hela_hiv_vif.tif`: https://media.scijava.org/scijava-ops/1.0.0/hela_hiv_vif.tif

0 commit comments

Comments
 (0)