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Biomedical-Imaging-Group/PSFGenerator 6

A Java software package to generate realistic 3D microscope Point-Spread Function (PSF)

deepimagej/deepImagej-ij2-plugin 4

DeepImageJ plugin coded with IJ2

Biomedical-Imaging-Group/Steer-n-Detect 2

ImageJ plugin - Steerable Template Detector

dasv74/imagej-plugin-model 0

Model to build a ImageJ model

dasv74/orientationj 0

OrientationJ: ImageJ plugins for directional image analysis. ///// Reference: Z. Püspöki et al., "Transforms and Operators for Directional Bioimage Analysis: A Survey," Springer International Publishing, 2016.

dasv74/template-imagej 0

Template for a ImageJ plugin (legacy)

dasv74/W_DS-i2K-IJNucleiSeg 0

BIAFLOWS workflow to segment clustered nuclei using a laplacian filter, thresholding and a binary watershed transform.

qjuppet/SingleCellClassifier 0

Single Cell Classifier (SCC) is an ImageJ/Fiji plugin that aims to classify cells based on features related to their nuclei and their neighbors.

issue closedBiomedical-Imaging-Group/IPLabImageAccess

Wrong visualization of small numbers in an image

When a number is given in scientific notation, the method visualize does not work properly. Moreover, some values are simply being erased. See example:

IPLabImageAccess {
  image: [ [ 3.061616997868383e-17, -0.5 ], [ 0.5, 3.061616997868383e-17 ] ],
  nx: 2,
  ny: 2,
  min: 0,
  max: 0,
  change_check: true
}
Result:
[[  3.06       ]
 [        3.06 ]]

While this does not hinder development, it is certainly urgent for the release of the labs

closed time in 9 hours

Alejandro-1996

issue commentBiomedical-Imaging-Group/IPLabImageAccess

Wrong visualization of small numbers in an image

It should now also work with scientific notation, very small and large numbers.

Alejandro-1996

comment created time in 9 hours

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Kay Lächler

commit sha ff8f94d0278662a6fadefd29ee746a672f2e47e5

Corrected visualize function to work with scientific notation

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issue openedBiomedical-Imaging-Group/OrientationJ

Problem with decimal separator in OrientationJ_DominantDirection

Hi, I use the plugin OrientationJ_Dominant_Direction in a macro to run over a directory of image. In the Log window A Ia a problem because the decimal separator is a coma and it also used to separate the numbers. Would it be possible to use the tab to separate the number ? t seems that only in line 96 (see below) comas have to be changes in \t Unfortunately I am not able to compile the corrected java file into a .class. Thank you

line 96 IJ.log(s1 + ", " + s2 + ", " + s3);

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esgomezm

commit sha 9d284c83313d4407c80d2a83f0d2d39f31021dbc

Update model.yaml

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release Biomedical-Imaging-Group/GlobalBioIm

v1.2

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created tagBiomedical-Imaging-Group/GlobalBioIm

tagv1.2

A unifying Matlab framework for the development of reconstruction algorithms (solving inverse problems) in computational imaging

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release Biomedical-Imaging-Group/GlobalBioIm

v1.2

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created tagBiomedical-Imaging-Group/GlobalBioIm

tagv1.2

A unifying Matlab framework for the development of reconstruction algorithms (solving inverse problems) in computational imaging

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ferreol soulez

commit sha e03488d4a423484b86c19974e7c2123f90f9a360

Deploy Biomedical-Imaging-Group/GlobalBioIm to github.com/Biomedical-Imaging-Group/GlobalBioIm.git:gh-pages

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E. Soubies

commit sha 4e9a791452690dc03734cf9a6715d0e31c1cff65

update NEWS.md

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E. Soubies

commit sha 192a346988f1495db2696d7c06291eb4b05c32b4

Prepare Doc for release

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ferreol soulez

commit sha 3fa76c570c9d8194cea7002cdc173519947446f6

Deploy Biomedical-Imaging-Group/GlobalBioIm to github.com/Biomedical-Imaging-Group/GlobalBioIm.git:gh-pages

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issue openedBiomedical-Imaging-Group/IPLabImageAccess

Wrong visualization of small numbers in an image

When a number is given in scientific notation, the method visualize does not work properly. Moreover, some values are simply being erased. See example:

IPLabImageAccess {
  image: [ [ 3.061616997868383e-17, -0.5 ], [ 0.5, 3.061616997868383e-17 ] ],
  nx: 2,
  ny: 2,
  min: 0,
  max: 0,
  change_check: true
}
Result:
[[  3.06       ]
 [        3.06 ]]

While this does not hinder development, it is certainly urgent for the release of the labs

created time in 21 days

pull request commentBiomedical-Imaging-Group/IPLabImageAccess

Make `normalize()` work

Hey, I am interested on participating with projects of any kind that relevant to biomedical imaging

smarter

comment created time in 22 days

pull request commentdeepimagej/models

add travis to verify-bioimageio-manifest

Thanks! Is this the same as in here, or do you need it to be in travis?

oh no, not at all. I didn't see that 👍

FynnBe

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PR closed deepimagej/models

add travis to verify-bioimageio-manifest
+0 -0

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FynnBe

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PR opened deepimagej/models

add travis to verify-bioimageio-manifest
+11 -0

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GollumEvent
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push eventBiomedical-Imaging-Group/IPLabImageAccess

Kay Lächler

commit sha b649962f6f7d7f8f984393eae598aaa975251a06

Added visualize function

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Kay Lächler

commit sha 68a114e9eb45f482fe7f095a19cefe2b481cb138

Merge branch 'master' of https://github.com/Biomedical-Imaging-Group/IPLabImageAccess

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issue openeddeepimagej/models

Linking to external objects

Some of our models are trained using ZeroCostDL4Mic notebooks. Those notebooks are also in the Bioimage.IO. It would be nice to have the connection between objects in the bioimage.io that do not necessarily belong to the same GitHub repository.

Example of our model: https://github.com/deepimagej/models/blob/6f65fb15f062ed2e4de3de7605aeb414c294a63e/manifest.bioimage.io.yaml#L81

which refers to this notebook: https://github.com/HenriquesLab/ZeroCostDL4Mic/blob/master/manifest.bioimage.io.yaml#L563

@oeway

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esgomezm

commit sha bed8ec248ff2e96df90b7e43a043610dccbc3d97

include dij notebooks of ZCDL4M

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pull request commentBiomedical-Imaging-Group/GlobalBioIm

Add Crop and Pad operator

my bad, your right. I will probably just add the negative index stuff and make alias.

FerreolS

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pull request commentBiomedical-Imaging-Group/GlobalBioIm

Add Crop and Pad operator

Yes there already exist. LinOpSelectorPatch (and its adjoint). We should avoid duplicate code. But you may create alias for more explicit naming if you want.

FerreolS

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PR opened Biomedical-Imaging-Group/GlobalBioIm

Add Crop and Pad operator

I though that we already have those Crop / Pad operators but I did not find them.

+227 -9

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Alejandro-1996

commit sha 6e81f297aa0d0ec9ecf05b933946e40a5871e9fa

Made iamge bigger and histogram smaller when 1 image is shown at a time

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ferreol soulez

commit sha 60343f320464e7d95a40ee260b6ad4ee150dbe6c

Deploy Biomedical-Imaging-Group/GlobalBioIm to github.com/Biomedical-Imaging-Group/GlobalBioIm.git:gh-pages

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ferreol soulez

commit sha 6e0f5564aae6172665cfd54c7875b0840495e026

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Ferreol

commit sha 7dbdaad069158775dda5a66c5c8beb669a8ceb48

previous iterate xold is no longer stored when it is not necessary

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Ferreol

commit sha 4b8b614b551a96f52da5dc5887a936bb73cff868

Save memory in ADMM

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Ferreol

commit sha 1c872726c7ad8a1cf302f9c4d6bbb26692a25259

Fix the cell sommation. Thanks Manu.

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Ferreol

commit sha 960e225d013440f3365dae16732eb206331a69ce

Add a test for TestCvgADMM()

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ferreol soulez

commit sha 2c68c7519bf36cafbcde4af6f447cf50af4e334c

Merge pull request #31 from FerreolS/ADMMSaveMem Save memory

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