Commits · master · IAH public / CellContactAnalyzer

29 Jan, 2020 12 commits
- Add a nice logo. · 232fdd36
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  232fdd36
- Use SciJava util to report plugin version. · b3b48d9a
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  b3b48d9a
- Properly offer not to track labels in the standalone plugin. · 99fc3a57
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  99fc3a57
- Rework the standalone plugin. · e2a17b89
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  e2a17b89
- New test drive for the standalone plugin. · fd291e7b
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  fd291e7b
- Rename test drive. · 326a23ef
  Jean-Yves TINEVEZ authored Jan 29, 2020
```
This one is for the integration with TrackMate.
```
  326a23ef
- Rename packages. · 7cf51ac7
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  7cf51ac7
- Revamp the contact img generator test drive. · 4c33e2c8
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  4c33e2c8
- .gitignore samples. · 96dd0fc2
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  96dd0fc2
- Revamp the interactive test. · d60799d6
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  d60799d6
- Fix calls to deprecated methods and useless @warnings. · ef466e9c
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  ef466e9c
- Update pom.xml. · a11aab32
  Jean-Yves TINEVEZ authored Jan 29, 2020
  
  a11aab32
03 Jul, 2018 5 commits
- Utility function. · df0be95a
  Jean-Yves TINEVEZ authored Jul 03, 2018
  
  df0be95a
- Build statistics on contacts only. · 7e47de02
  Jean-Yves TINEVEZ authored Jul 03, 2018
  
  7e47de02
- Detect correlation between contact formation and intensity spike. · e7c2c185
  Jean-Yves TINEVEZ authored Jul 03, 2018
  
  e7c2c185
- Clean trackmatcher. · 53feb9c0
  Jean-Yves TINEVEZ authored Jul 03, 2018
  
  53feb9c0
- Update parent pom to pom-scojava v21.0.0. · 8df3b347
  Jean-Yves TINEVEZ authored Jul 03, 2018
  
  8df3b347
08 Aug, 2017 1 commit
- TrackMatcher scripts generate data structure for forther analysis. · 7ed7291d
  Jean-Yves TINEVEZ authored Aug 08, 2017
  
  7ed7291d
04 Aug, 2017 2 commits
- trackmatcher: Harvest all contacts for a single calcium track. · f189b7e9
  Jean-Yves TINEVEZ authored Aug 04, 2017
  
  f189b7e9
- Fixes the trackmatcher MATLAB script for TrackMate scripts changes. · 1c435abb
  Jean-Yves TINEVEZ authored Aug 04, 2017
  
  1c435abb
03 Aug, 2017 1 commit
- Update pom to modern parent with its constraints. · 8edc5948
  Jean-Yves TINEVEZ authored Aug 03, 2017
  
  8edc5948
11 Jan, 2016 1 commit
- Add and use Anastassia colormap. · 0cd93912
  Jean-Yves TINEVEZ authored Jan 11, 2016
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  0cd93912
07 Jan, 2016 1 commit
- Add track labels in kymographs. · b249f0c7
  Jean-Yves TINEVEZ authored Jan 07, 2016
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  b249f0c7
12 Nov, 2015 6 commits
- Release v0.0.4. · 48a19188
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
* Fix crash caused by TrackMate v2.8.x update.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  48a19188
- Fix compile error du to TrackMate updated to v2.8.x · 0c6b5b32
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  0c6b5b32
- Update parent fiji pom to 16.2.0. · c1840230
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  c1840230
- Git ignore MATLAB backup files. · 48694811
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  48694811
- Display track names on trackmatcher output. · b52afa52
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  b52afa52
- Import the MATLAB script to match calcium tracks to contact tracks. · c9431274
  Jean-Yves TINEVEZ authored Nov 12, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  c9431274
15 Oct, 2015 7 commits

Bump to next development cycle. · f4ffecbb
Jean-Yves TINEVEZ authored Oct 15, 2015
```
v0.0.4-SNAPSHOT
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
f4ffecbb

Jean-Yves TINEVEZ authored Oct 15, 2015

Rework how contacts are made into spots in the TrackMate detector.
 * Spot radius represents the spot size (equivalent area of circle for
   2D, and volume of equivalent sphere for 3D).
 * Quality stores the total contact intensity in object.
 * The threshold paramter operates on the contact size (in pixels).
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>

a396f6be

Tweak UI and variable names a bit. · 5dcf7a91

Jean-Yves TINEVEZ authored Oct 15, 2015

Mainly rewrote some docs and change a variable name for clarity.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>

5dcf7a91

Change the spot creation strategy for CellContactDetector. · 9bcfef7d

Jean-Yves TINEVEZ authored Oct 15, 2015

Now spots are directly created from the mask of contacts. Their position
are the mean position of the pixel in each binary object, and we deduce
its radius from the object size. Quality value stores the total
intensity of the contact image within the object. The threshold is used
to discard contacts with a small size.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>

9bcfef7d

Generalize the thresholder class. · 156e0d7d
Jean-Yves TINEVEZ authored Oct 15, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
156e0d7d

Release v0.0.2. · 31fdb8c9

Jean-Yves TINEVEZ authored Oct 15, 2015

* Add a standalone plugin that generate contact image, mask and labels.
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>

31fdb8c9

Add an entry point for ImageJ Plugins menu. · e1a040bd
Jean-Yves TINEVEZ authored Oct 15, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
e1a040bd

09 Sep, 2015 4 commits
- Generate contact masks and labels. · 1093ff29
  Jean-Yves TINEVEZ authored Sep 09, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  1093ff29
- Add a standalone plugin that generates contact images. · a8f3eb02
  Jean-Yves TINEVEZ authored Sep 09, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  a8f3eb02
- Bump to next development cycle. · 6b79415d
  Jean-Yves TINEVEZ authored Sep 09, 2015
```
v0.0.2
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  6b79415d
- Release v0.0.1. · c05d054e
  Jean-Yves TINEVEZ authored Sep 09, 2015
```
Signed-off-by: Jean-Yves Tinevez <jean-yves.tinevez@pasteur.fr>
```
  c05d054e