Claude Nozères

Science Branch, Québec Region

Fisheries and Oceans Canada

Maurice Lamontagne Institute

claudenozeres@gmail.com

Overview

1. introduction: the guide (Tech. Rep. 2962)

2. image data: what is it about?

3. captures: preparations

4. metadata: why all the bother?

5. workflows: recipes for work

6. exports: archives & publishing

7. trends: comments on new tech.

8. questions: findings on the tour so far

afternoon: software demos & discussions

1. Introduction: background

Personal experiences – taking digital photos

of aquatic life since 2001

needed to document prey samples for marine

mammals, and film wasn‘t doing a good job

became aware of mixed information among users

○ frustrations were common when using either

consumer or industrial tools

○ by sharing experiences, our work may become

easier, and better quality image data is produced

Introduction: guide & tour

DFO‘s National Image Data Management

(NIDM) Working Group

fall 2010: began a ‗best practices guide‘ to assist

employees with their imaging work

mid-Dec. 2011, published the first full version:

Nozères. Tech. Rep. 2962, now online (WAVES)

Jan-Feb. 2012: tour of regions to introduce guide

○ the hope is that each site will then do a follow-up,

with advanced workshops, for their needs

Objectives: this talk1. to introduce a sample of common, but perhaps

misunderstood concepts in image data

2. to learn about your experiences with gear and software so we can share this with others in DFO

note: will also try

to include latest

information, not

in the guide

Headline: happy marine biologist

Keywords: scene, joke, smurf

Location: Belle-Isle

Category: personal

2. Image data – basic types

still image data (photo)

huge availability in consumer devices

well-established for industry & science but finicky?

moving image data (video)*

often consumer-oriented (family videos)

industrial applications: pricey and finicky?

information (metadata)

data about the image data

2008-08-07-

12:02:09...

*note: video is not discussed in this brief introduction – see guide for information

Why talk of files as ‗data‘?just another pretty picture

or an

aquatic species observation?Keywords: harbour seal, rock

Location: Sainte-Luce

Date: Sept. 8, 2009information

clearly visible

subjects

Image data: perceptions

‗If really so useful, we should all be doing it!‟

may end up generating stacks of fuzzy, dateless, unknown files = frustration

„I have enough science data to deal with‟

images as data may not be taken seriously

„I don‟t have time for more requirements!‟

learning about image data may be viewed as a time-waster instead of a work-saver

3. Capturing image data

camera settings

format (file type)

quality (lossy compression)

size (dimensions....)

special topic: geotagging (GPS data)

Camera settings: file

formats JPG (8-bit) is default, or only option for many good, but ‗baked‘ (limited for image editing)

RAW (10, 12, 14-bit) for advanced cameras require post-processing with RAW software

sometimes capture both ‗RAW+JPG‘

○ view JPG right away, store RAW for later edits

TIF is occasionally available (8 or 16-bit) microscope & tethered cameras, scanners

good choice for image analysis (16-bit)

‗baked‘ like JPG: harder to correct for whiteness

Camera settings:

‗quality’ (for JPG)

Lossy compression:

how much detail is to be

discarded in JPG?

Select quality:

„basic, good, fine, v.fine‟

= low to high quality

Lossless compression:

no data loss, no need to

set ‗quality‘ (RAW, TIF)

Settings: channels & bits

Channels Grayscale has 1 channel (black)

RGB (for screen) has 3: Red, Green, Blue

CMYK (for print) has 4: Cyan, Magenta, Yellow, blacK

Bits: levels, or gradation ‗steps‘ (in each channel) 1-bit = 21 = 2 values, on/off, black or white (like a fax)

8-bit = 28 = 256 values for tones (gray or colour images)

10, 12, 14, 16-bit = many thousands of tone levels

note: most monitors only display in 8-bit even if you can‘t see it, the data is there for analysis

Channels x

8-bit:

256 steps

black = 0

white = 256

Levels (tones)

16-bit:

65,536 steps

black = 0

white = 65,536

X

Why more bits matter

high-bit RAW & TIFF files have more tones

important in image analysis for feature (subject) discrimination, like plankton in a water sample

○ 16-bit grayscale may be preferred over 8-bit colour

the extra information enables powerful software editing (recover detail in light and dark areas)

○ JPG 8-bit can be also edited, but less dramatic

○ TIF at 8-bit has same limits (16-bit allows more)

○ RAW is >8-bit (e.g.,10-14)

Note: colour scanners may refer to 24-bit or 48-bit (3x8 or 3x16)

Settings: white balance

auto-white balance may be accurate, but sometimes better when set to conditions:

sunny, cloudy, shade, incandescent, fluorescent

JPG & TIF are ‗processed‘ files with their ‗whiteness‘ (white balance) set at capture

like a ‗Polaroid‘ instant photo: limited edits

RAW has metadata suggesting the setting, but is not fixed: can redo after capture

similar to a film negative: ‗reprocess it‘

Camera settings: white

balancecorrected file for white

Background should be white – clicked on it with a correction

tool and white balance was adjusted

RAW file: default capture

under fluorescent lights

Camera settings – size

...file size, image size (resolution), image re-sizing (pixel numbers),

pixel density, sensor size, sensor photosites, photostitching...

Camera settings – size

Image resolution

web or small: good for onscreen viewing

large (2 to 5 MP): good for regular prints

full-size (usually about 8 to 16 MP): archives

note: RAW is usually a full-size capture

Why choose for less than ‗full-size‘?

digital zoom (like cropping) sometimes handy

situations when a large image is a burden

○ documenting labels, geotagging, emailing

○ caution: set back to full-size afterwards

2600x1900

1600x1200

5 MP

2 MPweb

Size: pixels vs. files

Settings for size (or resolution) are about image

dimensions—how many megapixels (MP), not

the computer file size in Kilobytes, Megabytes

(KB, MB)

1600 (across) x 1200 (high) pixels = 2 MP

but file size will vary by format & compression

JPG with high compression = small file (68 KB)

TIFF with no compression = large file (5800 KB)

○ TIF with lossless compression of this image = (70 KB)

blank test

image 2 MP

Size: dimensions vs. density

on the computer: resizing is increasing or

decreasing the number of pixels (dimensions)

but sometimes we say we ‗resize‘ for print

really just setting pixel density (dots per inch: dpi)

image size (number of pixels) has not changed

larger dots: 72 dpi

upsized

(more pixels)original)smaller

(less pixels)

1600x12003600x2400

800x600

smaller dots: 300 dpi

Print viewing Screen viewing

Of sensor sizes &

megapixels Sensor size: physical dimensions (mm)

SLR cameras have large sensors

compact cameras have tiny image sensors

Photosites : density of sites on the sensor

two cameras may have the same resolution, but

the 12 megapixels of the SLR are over a much

wider area (the larger sensor) than the 12

megapixels on a small-sensor compact

Sensor sizes

Medium format &

full-frame 35mm

niche markets ($$)

slow development

smaller sensors

are versatile

extremely

competitive

intense

development

most

common

new Canon G1X

new Nikon 1

20-80 MP

12-24 MP

12-24 MP

5-16 MP

Sensor sizes

35 mm & Medium format ( & larger) are useful in aerial surveys (e.g., marine mammals) extreme level of fine, clean detail & tones

great for distances; macro work is trickier, bulky

most biology work is done with compacts or smaller (APS) SLRs: simpler, easier to use) compacts for macro work: many can do 0-10 cm

getting ‗pretty good‘ results: use software processing to beat physical limits, reduce noise

○ not ‗fakery‘ but sometimes undesired (see example later)

Capture tips: boost image size‘photostitching’

Capture tips

Consult

examples:

online image

galleries contrasting background

(white piece of plastic)

- gray and black also good

ruler or object in

view for scale

optional: have a colour card

(or something white) in view,

to correct for white balance

Capture: Geolocation

some cameras have internal GPS to embed coordinates & correct time zone date mostly in still cameras, but also some video (rare)

○ note: smartphones geotag both photos & videos

other cameras can have their images tagged with external data using, for example: 1) geotagged image at same location (e.g. smartphone)

2) GPS track and timestamp of image

○ note: image file must have correct clock time

○ tip: take a photo of the time on a GPS screen, then examine that photo‘s capture time info. to determine correction/adjustment for camera clock

Geolocation – image tagging

Camera with telephoto lens

(but no GPS)

Smartphone photo (tagged with GPS)Smartphone map (shows AIS)

Geolocation – image

taggingSmartphone photo

(tagged with GPS)

load into the geotagging software the

tagged photo with untagged photos

taken from the same location

SLR zoom photo

(geotagged w/phone image)

Keywords: ship, transport

Location: Sainte-Flavie

Category: personal

Geolocation – GPS track

sync record a GPS track log on an external device

log while taking camera images

later, download images and the GPS track

into geotagging software

the capture time of the photo will be used to

determine its position at that time on the

GPS track (‗sync‘)

embeds the coordinates into image file

NOTE: this is an example of image data information

(metadata), and not about image quality

4. Image (file) metadata

tags why the fuss over metadata? we may do ‗tagging‘ in order to be able to locate,

use, and credit the image files using the tags

where is the image metadata? camera files have well-known, standard places to

store this special text information

other image data, or non-standard information, may be entered in catalog files in a database system

do I need to do manually add all these tags? some are automatically included by the camera, such

as date, time, camera model (and GPS, if available)

Metadata tags: suggestions

Common fields for tagging images:

Filename: unique name (e.g, date-####.JPG)

Title: name for photo (but often for ID #)

Headline: short phrase about content

Description: more info. about content

Keywords: species name, subject

Location: place or station name

Creator: photographer‘s name

Filename:

20111014_IMG_1387.JPG

Title (catalog no.):

9682

Headline (quick describe):

Arctic isopods

Description/Caption (text on

paper label): Hand-collected

Mesidotea sabini from

Causeway at low tide, held in

an aquarium for one day

Keywords: Saduria sabini

Location: Frobisher Bay site 9

Creator: Claude Nozères

Tag example

useful, but not often done

Make sure your metadata makes sense to usersGood: added metadata

tags can be as you like

Bad: added metadata

tags can be as you like

Try to follow examples

of others, e.g. IPTC,

MWG, the DAM book

(some rules exist, but

most are open-ended)

Example:

Creator: unknown

Posted on blogs since 2010

Was able to find it using the

visible text in a Google search

How would you tag this image?

Title? Caption? Keyword?

Title: Rappahannock River,....

Description: (a literary quotation ?)

Source: Mike Ashenfelder, 2011

Metadata: retaining &

reading Older or simpler software may be unaware strip away camera metadata (capture date, etc)

Not all image browsing software play fair Apple, Microsoft, and Google are all competing to

make easy-to-use, popular tools

sometimes do hidden & proprietary processing ‗for your benefit‘ (automatically), which may be to the detriment of ‗industry-standard‘ metadata tags

recent examples: face recognition (all), geotagging (Windows Live), stripping of current tags (IPTC) with retired fields (Apple Aperture, iPhoto)

basic fields are easily read by most

advanced fields may be handy in projects

custom fields are available, but make sure

your users are aware of their existence

Metadata: summary for use

key lessons:

1) adopt a style and be consistent

2) let your users know what to expect

3) be vigilant for software behavior

5. Image data workflows

can we do editing and tagging without

worrying about how it works?

people want ‗recipes‘, or workflows

see guide no. 2962 for some examples

image data protocol examples

○ case studies for different work scenarios in

aquatic sciences

image data software examples

○ practical examples using software tools

Guide workflows: for discussion

the guide is not a

fixed set of rules

rather it is a list of

suggestions from

recent work

which ways of

working may be

easier (& better)

than others?

source: XKCD

(adapted

from The

Oatmeal)

Image

Data

work

it doesn’t

have to

hurt when

using the

right tools

(adapted

from The

Oatmeal)

Image

Data

work

it doesn’t

have to

hurt when

using the

right tools

Claude has

Quote overheard yesterday*

“How do you love Photoshop? Like someone

loves their wife,...or their cousin...or?”

“I love Photoshop like people love their kids –

no way to get rid of it, so I have to love it”

*Macworld Podcast – Less than Perfect: App Design

Image data work: a tale of 2

tools Adobe Photoshop (PS)....20+ years

classic tool for editing and....everything!

○ most folks only use it for a few tasks

Adobe Lightroom (LR)....5+ years

revolutionary workflow tool, now matured

○ ‗95%‘ of my photo work is now done inside LR

○ extra functions available with shareware plugins

Newsflash! Jan. 2012 – LR Public Beta 4:

video editing, geotagging, photobooks

Image data work: managing

tools Browsers: ‗find‘ your images on a workstation Windows Explorer (default – very limited)

Google Picasa (easy, basic, free)

Photoshop Bridge (full browser & metadata editor)

Photoshop Elements Organizer (new: object searching)

Cataloger & image editor Adobe Lightroom (workstation, not network use)

Catalogers Phase One Media Pro (workstation; free catalog reader)

Damnion, Canto Cumulus (network/server)

demonstrations this afternoon (bring your laptop)

6. Exporting: final work stages

After capturing, tagging, editing images,

we want to:

store the originals & edits (archiving)

distribute copies (publishing)

Exporting: archives

Ideally, this is about final edits in best

quality with metadata tags that are stored

securely in multiple locations and media

3-2-1 approach is recommended (Krogh)

have 3 copies (original & 2 backups in rotation)

store on 2 kinds of media (hard drive, DVD)

keep 1 off-site (not all stored same place)

This is an area that NIDM is working on: how to consolidate and preserve.

Large projects are likely good, but smaller ones may need advice

Exporting: galleries & print

may send re-sized versions:

800 pixel 72 dpi JPG is fine for web galleries, and especially for email

more-pixels, but at 150-300 dpi is for print (the density is important for clear prints)

for public viewing on web, review the file metadata & edit if desired

location, names, comments may be seen

edit in DAM (Bridge, MediaPro, LR)

Publishing – web CaRMS (Canadian Register

of Marine Species)

- online taxonomic resource with editors

- also has a user-added image gallery

- see Kennedy et al. Tech. Report

- note: camera metadata is visible

camera

metadata

added on

website

Publishing – web

DFO has several image

gallery projects

Coast Guard, SLGO,

CaRMS, CMB, others?

Groups may join a

large, existing gallery

Flickr is very popular and

does some metadata

used by EOL, BHL, GBIF

7. Trends: new camera

types before, chose either a digicam or a SLR small device & average images, or big rig & great

was a demand for quality and compact at same time

‗mirrorless interchangeable lens‘: MILC Panasonic, Olympus, Sony, Nikon, Pentax

2011: new disruptive trends in compacts ‗retro-style‘: Olympus Pen, Fujifilm X100, X10...

‗ultra-modern‘ camera phones: iPhone 4S

2012: light field (Lytros) – ‗refocus anytime‘

large-sensor

MILC

large-sensor

fixed compact

tiny-sensor

fixed compact

lightfield (Lytros)

New tech: changing the

game editing software

new camera types

high-sensivity sensors (lowlight)

solid-state memory (‗flash‘)

cheap hard drives

network storage (‗cloud‘, e.g., Dropbox)

tablets & tactile displays (iPad, Cintiq)

not just fashion: new types may lead to better image

data and much improved workflow (easier & faster)

New tech: science benefits

lowlight sensors: reduce need to carry lights fewer noisy, blurry (slow shutter) shots

compacts: easier to carry & use capture events more often in the field

SSD: insensitive to ship vibration, magnets use on underwater towsleds, aerial surveys

large drives: save all, do backups don‘t bother to delete or waste $$ time reviewing

cloud services: share files with colleagues don‘t burden email with huge attachments

tablets: field guides, rapid data entry & review

Newer is not

always betterPentax had long line of WP cameras,

but recent models not good indoors

Sony & Panasonic are new entrants,

but are giving much better files

Late 2011 DPReview test: indoors w/flash photo

clean detail

clean detail

mushy when indoors

new Pentax Optio when used indoors:

mushy photo—hard to identify

Canon Powershot: clean detail,

easier to identify small organisms

Teleost Aug. 2011

Resources – websites

The Luminous Landscape – practical opinions

The DAM Book forum – ―real DAM answers‖

dpBestflow.org – best practices & workflows

JISC Digital Media – advice & examples

Digital Photography Review (dpreview.com)

WHOI HabCam – underwater photo

SERPENT projet – underwater video

CARMS Photogallery – species images

Resources – books

The DAM Book, 2nd edition, Krogh

Photoshop CS5 and Lightroom 3: A Photographer‟s Handbook, Laskevitch

Adobe Photoshop Lightroom 3: the missing FAQ, Brampton

Photographic Multishot Techniques, Steinhoff & Steinhoff

The VueScan Bible, Steinhoff

On Digital Photography, Johnson

Resources – documents

(PDF) GBIF Community Site: Best Practices Manuals

Federal Agencies Digitization Initiative (FADGI),

Still Image Working Group

Metadata Working Group (MWG)

IPTC Image Metadata Handbook

Establishing best practices for marine biological

data, Seeley et al. 2008, COWRIE

CaRMS photogallery user guide, Kennedy et al.

2011. DFO Tech. Rep. 2933

Resources – software utilities

Ingestamatic, Photographer‘s Toolbox,

JFriedl‘s Lightroom Goodies, Photo

Mechanic, DVMP, CatDV, RoboGEO,

Cineform, Clipwrap, Helicon Focus,

CDFinder, CDWinder, NIS Elements

freeware: Picasa, ImageJ, VLC, VARS,

ExifTool, IrfanView, Zooscan, Shotwell,

Handbrake, Contour Storyteller, MPEG

Streamclip

Obj. 2: learning – Sault-Ste-

Marie Otolith microscopy w/Image Pro (5 MP) good file naming, 3-2-1 storage; might try tagging

Scanning historical slides of activities (size?..) all notes are entered in filename – need to rethink this

Underwater video for lamprey control (volume?) proprietary DVR: take video feed over RCA & capture

Underwater dam inspection using a 2 m pole want live view & record; suggest using 2 dif. cameras

Photo folder on local server (8 GB) do temp. catalog to browse, then do perm. catalog

Obj. 2: learning – Nanaimo

Otoliths: want to overlay 2 images, & dots need 3rd party tools (Photoshop, ImageJ)

Import prior analyses (keywords into LR) LR plugin (Syncomatic: based on filenames)

Reading catalog without full software LR: not usually. ExMedia/Media Pro: Yes

Can we use alternative ingestion (import) tools? Yes, Photo Mechanic, Ingestamatic may be useful for high

volume, batch file entry (e.g., marine mammal surveys)

Easy way to get started and using tools like LR? Various resources – our guide is an example, but we still

need a forum or other place to post experiences and tips

Obj. 2: learning – Burlington

Q‘s does DFO have a site licence for this software?

how to distribute a catalog on the network?

can I use custom annotation fields in a catalog?

what kind of scanner to archive histology slides?

Flowcam produces a composite of plankton shots in

sample: how to manage?

Nikon imaging microscope produces custom files –

how to manage?

How to transfer hierarchical folder names into

annotation fields? ...and more!

Obj. 2: learning – St.

Andrews geomatics & video lab: of screens & mice

had a quality monitor, but not great for viewing

charts or when using a mouse and keyboard to

trace habitats at same time as viewing images

solution: use the right display for different work:

1) HDTV for video (1920x1080 pixels)

2) 27in NEC for photos (2560 x1600 pixels)

3) 24in tactile display (Wacom Cintiq) for tracing

habitat classifications—more efficient

Obj. 2: learning – St.

Andrews reusing legacy & custom equipment

big HDV camcorder, with $30K UW housing

○ don‘t want to buy a new camera & $$$ housing

solution: HDMI video out to flash memory cards

result: instant digital video (no tape playback to

import), and higher quality (original video

capture, not compressed to fit HDV tape)

Obj. 2: learning – St. John‘s

need a place to obtain and learn more

want workshops, website forums....CMB?...

exchange files with remote fisher. observers

receive and send feedback on species ID images

cloud computing seen as a solution (Dropbox)

have to enable software updates

older software versions (>3 yrs.) are not aware of

current metadata and image file standards

want access to image files for regional guides

other regions may do ID books, want to do it here