ijtiff

ijtiff: An R package providing TIFF I/O for ImageJ users - Published in JOSS (2018)

https://github.com/ropensci/ijtiff

Science Score: 93.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
○
Committers with academic emails
○
Institutional organization owner
✓
JOSS paper metadata
Published in Journal of Open Source Software

Keywords

image-manipulation imagej peer-reviewed r r-package rstats tiff-files tiff-images

Keywords from Contributors

crypto-currency-exchanges exploratory-data-analysis missingness ropensci visualisation

Last synced: 4 months ago · JSON representation

Repository

An R Package for general purpose TIFF file I/O which plays nice with ImageJ

Basic Info

Host: GitHub
Owner: ropensci
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/ijtiff
Size: 58.1 MB

Statistics

Stars: 17
Watchers: 5
Forks: 9
Open Issues: 1
Releases: 23

Topics

image-manipulation imagej peer-reviewed r r-package rstats tiff-files tiff-images

Created almost 8 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing Codemeta

README.Rmd

---
output: github_document
---



```{r setup, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
original_files <- dir()
```

# ijtiff  

[![R-CMD-check](https://github.com/ropensci/ijtiff/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/ijtiff/actions)
[![codecov](https://app.codecov.io/gh/ropensci/ijtiff/graph/badge.svg?token=rNNRw2FU0F)](https://app.codecov.io/gh/ropensci/ijtiff)

[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)

[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ijtiff)](https://cran.r-project.org/package=ijtiff)
![RStudio CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/ijtiff)
![RStudio CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/ijtiff)

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00633/status.svg)](https://doi.org/10.21105/joss.00633)


## Introduction

This is a general purpose TIFF I/O utility for R. The [`tiff` package](https://cran.r-project.org/package=tiff) already exists for this purpose but `ijtiff` adds some functionality and overcomes some bugs therein. 

* `ijtiff` can write TIFF files whose pixel values are real (floating-point) numbers; `tiff` cannot. 
* `ijtiff` can read and write _text images_; `tiff` cannot.
* `tiff` struggles to interpret channel information and gives cryptic errors when reading TIFF files written by the _ImageJ_ software; `ijtiff` works smoothly with these images.

To learn about `ijtiff` and how to use it, visit the package website at https://docs.ropensci.org/ijtiff/.


## Installation

### `libtiff`

`ijtiff` requires you to have the `libtiff` C library installed. To install `libtiff`:

* On __Debian Linux__, try `sudo apt-get install libtiff-dev libbz2-dev libdeflate-dev liblzma-dev libwebp-dev libzstd-dev zlib1g-dev`.
* On __Fedora Linux__, try `sudo yum install libtiff-devel libbz2-devel libdeflate-devel liblzma-devel libwebp-devel libzstd-devel zlib-devel`.
* On __Mac__, you need [Homebrew](https://brew.sh/). Then in the terminal, run `brew install libtiff`.
* On __Windows__, no setup is required.


### Installing the release version of the `ijtiff` R package

You can install `ijtiff` from CRAN (recommended) with:
```{r CRAN-installation, eval=FALSE}
install.packages("ijtiff")
```


### Installing the development version of the `ijtiff` R package

You can install the development version from GitHub with:
```{r GitHub-installation, eval=FALSE}
devtools::install_github("ropensci/ijtiff")
```


## Acknowledgement
This package uses a lot of code from the original `tiff` package by Simon Urbanek.


## Contribution
Contributions to this package are welcome. The preferred method of contribution is through a github pull request. Feel free to contact me by creating an issue. Please note that this project is released with a [Contributor Code of Conduct](https://github.com/ropensci/ijtiff/blob/master/CONDUCT.md). By participating in this project you agree to abide by its terms.

```{r cleanup, include = FALSE}
new_files <- setdiff(dir(), original_files)
file.remove(new_files)
```

[![ropensci_footer](https://ropensci.org/public_images/ropensci_footer.png)](https://ropensci.org)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

JOSS Publication

ijtiff: An R package providing TIFF I/O for ImageJ users

Published

March 16, 2018

DOI

10.21105/joss.00633

Volume 3, Issue 23, Page 633

Authors

Rory Nolan

Wellcome Centre Human Genetics, University of Oxford

Sergi Padilla-Parra

Wellcome Centre Human Genetics, University of Oxford, Department of Structural Biology, University of Oxford

Editor

Arfon Smith

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Papers & Mentions

Total mentions: 1

SAPHIR: a Shiny application to analyze tissue section images

DOI: 10.12688/f1000research.27062.2
OpenAlex ID: https://openalex.org/W3095718674
Published: April 2021

Last synced: 2 months ago

GitHub Events

Total

Create event: 3
Release event: 2
Issues event: 2
Delete event: 1
Issue comment event: 6
Push event: 48
Pull request event: 1

Last Year

Create event: 3
Release event: 2
Issues event: 2
Delete event: 1
Issue comment event: 6
Push event: 48
Pull request event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 260
Total Committers: 5
Avg Commits per committer: 52.0
Development Distribution Score (DDS): 0.181

Past Year

Commits: 35
Committers: 2
Avg Commits per committer: 17.5
Development Distribution Score (DDS): 0.029

Top Committers

Name	Email	Commits
Rory Nolan	r**n@g**m	213
Rory Nolan	r**y@m**m	35
Jeroen Ooms	j**s@g**m	9
Maëlle Salmon	m**n@y**e	2
muschellij2	m**2@g**m	1

Committer Domains (Top 20 + Academic)

mirvie.com: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 17
Total pull requests: 8
Average time to close issues: 4 months
Average time to close pull requests: 9 days
Total issue authors: 12
Total pull request authors: 3
Average comments per issue: 4.06
Average comments per pull request: 2.5
Merged pull requests: 7
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: about 5 hours
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

maelle (4)
rorynolan (2)
naikymen (2)
Marc-Girondot (1)
DaphneW-AkoyaBio (1)
Enchufa2 (1)
gitdemont (1)
diuming (1)
horndog (1)
hadley (1)
sckott (1)
mirvie (1)

Pull Request Authors

jeroen (6)
maelle (1)
muschellij2 (1)

Top Labels

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Packages

Total packages: 1
Total downloads:
- cran 1,272 last-month
Total docker downloads: 88,660

Total dependent packages: 5
Total dependent repositories: 6
Total versions: 38
Total maintainers: 1

cran.r-project.org: ijtiff

Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files

Homepage: https://docs.ropensci.org/ijtiff/
Documentation: http://cran.r-project.org/web/packages/ijtiff/ijtiff.pdf
License: GPL-3
Latest release: 3.1.3
published 9 months ago

Versions: 38
Dependent Packages: 5
Dependent Repositories: 6
Downloads: 1,272 Last month
Docker Downloads: 88,660

Rankings

Docker downloads count: 0.0%

Forks count: 6.8%

Dependent packages count: 8.2%

Average: 8.9%

Dependent repos count: 11.9%

Stargazers count: 12.5%

Downloads: 14.0%

Maintainers (1)

rorynoolan@gmail.com

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 3.5 depends
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methods * imports
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spelling * suggests
testthat >= 2.1 suggests
tiff * suggests
vdiffr * suggests

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r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

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actions/checkout v3 composite
actions/upload-artifact v3 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ijtiff

Science Score: 93.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

JOSS Publication

ijtiff: An R package providing TIFF I/O for ImageJ users

Authors

Editor

Tags

CodeMeta (codemeta.json)

Papers & Mentions

SAPHIR: a Shiny application to analyze tissue section images

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

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cran.r-project.org: ijtiff

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Maintainers (1)

Dependencies