Fiji module for image transformation and related algorithms
CellProfiler/CellProfiler-plugins 33
Community-contributed and experimental CellProfiler modules.
Plugins for bone image analysis
Fork of Java Curses 0.9.5 that builds using Maven and CMake
Jupyter notebooks for CellProfiler and friends
My configuration files
Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment (particularly UW-Madison LOCI and Glencoe Software). Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
My personal scripts
ctrueden/finite-state-machines 2
Nondeterministic Finite Automaton Simulator
Hack your GitHub contributions calendar. UNFINISHED
startedcgohlke/imagecodecs
started time in 3 hours
push eventscijava/pom-scijava
commit sha 472bcc4a1425c84ba7b731bb39d321749a32c224
Bump imglib2-roi -> 0.11.0
push time in 5 hours
created tagimglib/imglib2-roi
Regions of interest (ROIs) and labelings for ImgLib2
created time in 5 hours
push eventimglib/imglib2-roi
commit sha f1e5daae75cab827790293b0bd9c9859f160d7c8
Bump to next development cycle Signed-off-by: Mark Hiner <hinerm@gmail.com>
push time in 5 hours
push eventimglib/imglib2-roi
commit sha 39e16ef051e1ed776059fb4728b6cf5f8bc237cd
Bye bye 2020!
push time in 5 hours
push eventimglib/imglib2-roi
commit sha 4e80eb5511d4b51eef932b0563a27ab49dbb9631
Increase minor version 96f454cb5f6f506825b69d24149dc997ea5e4c31 adds new API
push time in 5 hours
push eventimglib/imglib2-roi
commit sha e7f6f0cc8561d00736b665aa686ef6d199b58abd
Bump pom-scijava to 30.0.0 RealIntervals now validate their own dimensions, so we do not have to add a layer of checking on top.
push time in 5 hours
push eventscijava/pom-scijava
commit sha a57badca9296d3dbbb768ebe0c5d0d75a5ed0c23
Bump TrakEM2 -> 1.3.5
push time in 5 hours
issue commenttrakem2/TrakEM2
Yes! see #25 (07d67a9?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.
@tferr oh perfect. I opened https://github.com/trakem2/TrakEM2/pull/28 which includes your changes and updates the pom as well, now that we have something to pin to.
comment created time in 5 hours
pull request commenttrakem2/TrakEM2
@acardona @axtimwalde
This PR includes and can replace https://github.com/trakem2/TrakEM2/pull/25
Can you merge this and cut a new minor release? Then I can make a new pom-scijava and get everything into Fiji.
comment created time in 5 hours
fork hinerm/TrakEM2
ImageJ plugin for morphological data mining, 3D modeling and image stitching, registration, editing and annotation.
fork in 5 hours
push eventscijava/pom-scijava
commit sha 94ab25f30ce5e951a6e8d9daf7ab5e3badc23978
Bump component version multiview-reconstruction -> 0.9.3
push time in 5 hours
issue closedfiji/fiji
How can I save 16 bit images sequence to amira ascii format
How can I save 16 bit images sequence to amira ascii format. Works when images are 8 bits.
closed time in 14 hours
gitlabspy
startedjzy3d/jzy3d-api
started time in 20 hours
issue commenttrakem2/TrakEM2
Yes! see #25 (https://github.com/trakem2/TrakEM2/pull/25/commits/07d67a947fd7c23d2b608c4b46b55f50338482cf?diff=split&w=1). The PR may be a bit outdated, but it does exactly that.
comment created time in 21 hours
fork hinerm/multiview-reconstruction
Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data
fork in a day
push eventfiji/fiji-lib
commit sha c6647c9fdd04a548cab7cd60846a8d7bf3fa620f
Bump to pom-scijava 30.0.0 This is not strictly necessary, but pom-scijava 12.0.0 + pom-scijava-base 2.0.0 do not have a version property for net.imagej:ij, instead using the older imagej1.version, which can make attempts at overriding the version unexpected.
push time in a day
issue commenttrakem2/TrakEM2
@tferr can you suggest an alternative? Or can we re-introduce that method?
I am assuming the individual X-Y-Z methods can be looped over from 0..result.size()?
comment created time in a day
issue commenttrakem2/TrakEM2
https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L716
This can be replaced by result.size().
https://github.com/trakem2/TrakEM2/blob/94e44580ebecafe036aeb96fa3150b7e4fa6f7af/src/main/java/ini/trakem2/display/Polyline.java#L717
That one is more difficult. The getXYZUnscaled() method was removed here:
https://github.com/morphonets/SNT/commit/8f74838884911f4276b09764372d277378872ba4#diff-9d18d39571ccc3273052cc8eb8a38f88b03cb2ef6edccde1f06956dab28288ae
@tferr can you suggest an alternative? Or can we re-introduce that method?
comment created time in a day
issue commenttrakem2/TrakEM2
Polylineis part of TrakEM2.
argh. Of course, thank you. Polyline itself needs its imports updated to the new packages:
import sc.fiji.snt.Path;
import sc.fiji.snt.SearchInterface;
import sc.fiji.snt.SearchProgressCallback;
import sc.fiji.snt.TracerThread;
And these lines need to be updated for changed API/field visibility.
comment created time in a day
push eventscijava/scijava-common
commit sha f6d8749965411a07c9ec96029ad2991620626a1a
Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415
commit sha b15807535d2822c3a0e1d69040f21267ff6cd989
TypesTest: test for array types with generics
commit sha c7aa9f497534cb23765a8af80b4d4caa117d3a05
adds test for string to array conversion in command
commit sha 46ca0d04c5c86eeb51f9daa9f130b0d7c8decd65
Bump pom-scijava to 30.0.0
commit sha 971ec96226cf7a146ff484cb58f21df6611269d0
Improve error message for missing required inputs Human-friendly names can be registered at runtime by calling ObjectService#addHumanFriendlyName(Class, String).
push time in a day
push eventscijava/scijava-common
commit sha f6d8749965411a07c9ec96029ad2991620626a1a
Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415
commit sha b15807535d2822c3a0e1d69040f21267ff6cd989
TypesTest: test for array types with generics
commit sha c7aa9f497534cb23765a8af80b4d4caa117d3a05
adds test for string to array conversion in command
commit sha 46ca0d04c5c86eeb51f9daa9f130b0d7c8decd65
Bump pom-scijava to 30.0.0
commit sha 0fc27eb79b24c814d673355503ecd12482a8b92f
ScriptService: add getScript(String,String) signature This makes it easier to retrieve a ScriptInfo object from a script string (without going via File). Closes #389.
push time in a day
push eventscijava/scijava-common
commit sha f6d8749965411a07c9ec96029ad2991620626a1a
Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415
commit sha b15807535d2822c3a0e1d69040f21267ff6cd989
TypesTest: test for array types with generics
commit sha c7aa9f497534cb23765a8af80b4d4caa117d3a05
adds test for string to array conversion in command
commit sha 46ca0d04c5c86eeb51f9daa9f130b0d7c8decd65
Bump pom-scijava to 30.0.0
commit sha 34719d5ae6d7cc3b04fc50ae6b48642922f3bd5c
Add support for #@import directive
push time in a day
push eventscijava/scijava-common
commit sha f6d8749965411a07c9ec96029ad2991620626a1a
Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415
commit sha b15807535d2822c3a0e1d69040f21267ff6cd989
TypesTest: test for array types with generics
commit sha c7aa9f497534cb23765a8af80b4d4caa117d3a05
adds test for string to array conversion in command
commit sha 46ca0d04c5c86eeb51f9daa9f130b0d7c8decd65
Bump pom-scijava to 30.0.0
commit sha bd70ed02cc2d457dac53a875715832cd4c3d218b
Fix javadoc of ObjectIndex Remove redundant paragraph.
push time in a day
push eventscijava/scijava-common
commit sha f6d8749965411a07c9ec96029ad2991620626a1a
Fix Types.raw for GenericArrayType Also add minimal test for array types with generics. See https://github.com/scijava/scijava-common/issues/415
commit sha b15807535d2822c3a0e1d69040f21267ff6cd989
TypesTest: test for array types with generics
commit sha c7aa9f497534cb23765a8af80b4d4caa117d3a05
adds test for string to array conversion in command
commit sha 46ca0d04c5c86eeb51f9daa9f130b0d7c8decd65
Bump pom-scijava to 30.0.0
commit sha c8ab4ad9ae0f76588ea92e61c741a703a94d7f19
DefaultWidgetModel: check for null choicesList Let's fail fast and return null when item.getChoices() returns null.
push time in a day