profile
viewpoint
Cameron Lloyd camlloyd University of Debrecen Debrecen, Hungary RA @CellMoTher

warpling/Macmoji 1588

Slack/GitHub/Trello emoji for your mac! 😁 💥 💻

camlloyd/angiotool 0

A trial to convert AngioTool ( https://ccrod.cancer.gov/confluence/display/ROB2/Home ) into a Fiji plugin

camlloyd/bioformats2raw 0

Bio-Formats whole slide imaging to raw format converter

camlloyd/deepimagej-plugin 0

The ImageJ plugin to run deep-learning models

camlloyd/imagej 0

:sparkler: Open scientific N-dimensional image processing :microscope:

camlloyd/imagej-common 0

ImageJ core data model

camlloyd/imagej-launcher 0

The ImageJ native launcher

camlloyd/imagej-legacy 0

Backwards compatibility with ImageJ 1.x

camlloyd/imagej.github.io 0

GitHub Pages for ImageJ

camlloyd/ISIC-Archive-Downloader 0

A script to download the ISIC Archive of lesion images

push eventscijava/pom-scijava

Mark Hiner

commit sha 472bcc4a1425c84ba7b731bb39d321749a32c224

Bump imglib2-roi -> 0.11.0

view details

push time in 4 hours

push eventscijava/pom-scijava

Mark Hiner

commit sha a57badca9296d3dbbb768ebe0c5d0d75a5ed0c23

Bump TrakEM2 -> 1.3.5

view details

push time in 5 hours

push eventscijava/pom-scijava

Mark Hiner

commit sha 94ab25f30ce5e951a6e8d9daf7ab5e3badc23978

Bump component version multiview-reconstruction -> 0.9.3

view details

push time in 5 hours

issue commentqupath/qupath

Exception when resetting an annotation description

I've fixed this bug on my branch like this: https://github.com/yli-hallila/qupath/blob/master/qupath-core/src/main/java/qupath/lib/objects/PathAnnotationObject.java#L77-L81

petebankhead

comment created time in 6 hours

issue commentglencoesoftware/bioformats2raw

0.3.0

master bumped to 0.3.0-SNAPSHOT in 030bfd285907ee95d471cf5313001c6ddb260467.

chris-allan

comment created time in 8 hours

push eventglencoesoftware/bioformats2raw

Chris Allan

commit sha 030bfd285907ee95d471cf5313001c6ddb260467

Bump version to 0.3.0-SNAPSHOT

view details

push time in 8 hours

issue openedglencoesoftware/bioformats2raw

0.3.0

Follow on from discussion on #78. Major version checklist:

  • [ ] Bump master to 0.3.0-SNAPSHOT
  • [ ] Document the removal of N5 support and merge #78
  • [ ] Document changes to command line arguments
  • [ ] Bump layout version
  • [ ] Update layout based on suggestions from #78 (will have an effect on isyntax2raw and raw2ometiff)
  • [ ] Document existing layout and changes to layout

/cc @melissalinkert, @joshmoore

created time in 8 hours

issue commentmpicbg-csbd/stardist

StarDist (2D) on GPU in Exclusive Process mode

Hey @maweigert,

Thank you for testing. According to the nvidia-manual:

sudo nvidia-smi -i 0 -c EXCLUSIVE_PROCESS

will set GPU 0 to exclusive process mode. I currently do not have access to a GPU-machine on which I can run as super-user, so I cannot test if

suda nvidia-smi -c 0

would do the trick, too.

Regarding 2.: No, it does not throw an error.

Best, D

dsethz

comment created time in 8 hours

issue openedqupath/qupath

Exception when resetting an annotation description

Bug report

Describe the bug In v0.2 it isn't possible to set an annotation description, then reset it (by removing the text).

To Reproduce Steps to reproduce the behavior:

  1. Create an annotation
  2. Change the description in the properties and apply the change
  3. Delete the description and (try to) apply the change

Alternatively use this script:

def roi = ROIs.createRectangleROI(0, 0, 100, 100, ImagePlane.getDefaultPlane())
def annotation = PathObjects.createAnnotationObject(roi)
annotation.setDescription("something")
annotation.setDescription(null)

Expected behavior Setting description to null or an empty string removes it.

Desktop (please complete the following information):

  • QuPath Version 0.2

Additional context See https://forum.image.sc/t/unable-to-clear-annotation-description-in-qupath/47741

Should be quite straightforward to fix, but subtleties take a bit of thought.

created time in 9 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

pull request commentimagej/imagej-updater

extend error message with a link to the forum

How about creating a new topic ImageJ FAQ on the forum, where we can group frequently asked questions like this one, and then link to it with a more concise link?

Related: we used to have https://imagej.net/FAQ as well, but it's currently still read-only, and will likely take a while before the wiki is fully migrated.

haesleinhuepf

comment created time in a day

startedSebastienTs/MosaicExplorerJ

started time in a day

push eventscijava/pom-scijava

Mark Hiner

commit sha b178a0b8d0d1c6efe87dada2c034930021619991

Bump component version scijava-common -> 2.86.1

view details

push time in a day

PR opened imagej/imagej-updater

extend error message with a link to the forum

Hi @frauzufall, @ctrueden,

I would like to add a link to the forum to an error message. We are repeatedly answering that question on the forum and I think it might help to have that short-cut directly in the error message.

Let me know what you think!

Cheers, Robert

+2 -1

0 comment

1 changed file

pr created time in a day

fork haesleinhuepf/imagej-updater

The automatic updater for ImageJ

fork in a day

issue openedsaalfeldlab/bigwarp

Respect unit when applying transform

From the presentation at NEUBIAS Academy by @bogovicj:

When applying the transform to the moving image, the spatial calibration is correct, but the unit might get wrong (e.g. µm instead of nm).

created time in a day

issue commentmpicbg-csbd/stardist

CPU memory usage keeps on increasing during training

Hello Stardist team,

Thank you for your work! Unfortunately, I still have a memory issue even using @maweigert proposal.

Firstly, you can see just below the memory increase that I faced:

Epoch 20 Beginning

16:32:22 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      278769       45396         368       61033      103489
Swap:          8191        5230        2961


Epoch 20 End 

16:33:16 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      283010       41155         368       61033       99248
Swap:          8191        5230        2961


Epoch 25 Beginning

16:34:33 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      284364       39797         368       61038       97894
Swap:          8191        5230        2961


Epoch 25 End 

16:39:46 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      287205       36955         368       61038       95053
Swap:          8191        5228        2963

 

Epoch 30 Beginning

16:41:14 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      289252       34906         368       61041       93008
Swap:          8191        5228        2963


Epoch 30 End 

16:47:35 [lsancere@sulaco TensorFlowGPU]# free -m
              total        used        free      shared  buff/cache   available
Mem:         385200      293019       31139         368       61041       89240
Swap:          8191        5228        2963

Regarding what you proposed, we add the following lines in our code to use a dynamic sequence:

ind = rng.permutation(len(Raw))
self.X= self.DataSequencer(Raw, self.axis_norm, Normalize = True, labelMe = False)
self.Y= self.DataSequencer(RealMask, self.axis_norm, Normalize = False, labelMe = True)

n_val = max(1, int(round(0.15 * len(ind))))
ind_train, ind_val = ind[:-n_val], ind[-n_val:]

self.X_val, self.Y_val = [self.X[i] for i in ind_val]  , [self.Y[i] for i in ind_val]
self.X_trn, self.Y_trn = [self.X[i] for i in ind_train], [self.Y[i] for i in ind_train]

With the following DataSequence class:

class DataSequencer(Sequence):
         
         
            def __init__(self, files, axis_norm, Normalize = True, labelMe = False):
                super().__init__() 
                
                self.files = files
               
                self.axis_norm = axis_norm
                self.labelMe = labelMe
                self.Normalize = Normalize
                
            def __len__(self):
                return len(self.files)
            
            
            def __getitem__(self, i):
                
                        #Read Raw images
                         if self.Normalize == True:
                                 x = ReadFloat(self.files[i]) 
                                 x = normalize(x,1,99.8,axis= self.axis_norm) 
                         if self.labelMe == True:
                                 #Read Label images
                                 x = ReadInt(self.files[i])
                                 x = label(x)
                   
                         return x

ReadFloat and ReadInt are the following:

def ReadFloat(fname):

    return imread(fname).astype('float16')         
         

def ReadInt(fname):

    return imread(fname).astype('uint16')  

The training images have size between 384 by 384 pixels to 4000 by 4000 pixels and we choose a patch size of 384 by 384 in out training with 128 Rays. Total number of Images = 4216

Do you have any clues about this memory increase?

Thank you for your support.

MLbyML

comment created time in a day

issue closedscijava/pom-scijava

Imagej version points to non-existant version

https://github.com/scijava/pom-scijava/blob/bed338cc73b46ddc104a4e871537803f700e2461/pom.xml#L419

closed time in a day

kephale

issue commentscijava/pom-scijava

Imagej version points to non-existant version

These versions exist now!

kephale

comment created time in a day

push eventimagej/list-of-update-sites

Travis CI

commit sha 828210b454574458806489b105f37d4b8e8a4cd0

Update list of update sites (Travis build 690)

view details

push time in a day

push eventimagej/list-of-update-sites

Kyle Harrington

commit sha 7f304183257232e48959ce3bebc913dedcc2cc12

Replace deprecated Radial Symmetry update site with new update site

view details

Deborah Schmidt

commit sha 62d613c9ea4b44481da9e4b6a09356bd4f7809bd

Merge pull request #67 from ida-mdc/master Replace deprecated Radial Symmetry update site with new update site

view details

push time in a day

push eventraphaelhanneken/apple-juice

Raphael Hanneken

commit sha 8cab2a1034550a1ced54c42bd2731855f9f892d5

update project.pbxproj

view details

push time in a day

push eventsaalfeldlab/bigwarp

bogovicj

commit sha 0f6c0a67abe8540a06c16e1c72cd787e54e04713

update bigwarp n5 script

view details

push time in a day

issue commentwarpling/Macmoji

Install script no longer installs on Mac OS X Catalina 10.15

Hey @bval, super sorry for never getting back to you. I spent a day trying to get the old bash script working again but would like to migrate it to AppleScript or Python. How do you imagine an Apple Script being able to import them into PrefPane? I'm not terribly familiar.

Also where is com.apple.TextInput? I don't see it under ~/Library/Preferences/

bval

comment created time in a day

push eventdeepimagej/deepimagej-plugin

carlosuc3m

commit sha f415e307ae1977f3a0f3d8eb3d7253aed541c512

Add more information at the begining of DIJ Run All changes for DIJ Run - Show model even if the model.yaml is wrong. If it is the case, tell the user when the model is selected and show which fields are missing - Show model even if sha256 does not coincide. If it is the case, tell the user when the model is selected - Show loading screen at the begining tellin the user which model is being loaded and whether tf or pt is being loaded

view details

push time in 2 days

starteduhlmanngroup/splinedist

started time in 2 days

fork haesleinhuepf/ezomero

A module with convenience functions for writing Python code that interacts with OMERO.

fork in 2 days

startedTheJacksonLaboratory/ezomero

started time in 2 days

more