11/6/97

3D reconstruction from TEM images requires high resolution digital

images. With the use of scanners with spot sizes of down to 7 microns

a single sheet of em film produces a huge image file. With the need

to collect hundreds/thousands of such images to improve

resoultion/noise in reconstructs what are peole doing to store all

these files?

The files need to be stored so that they can be retrieved sensibly so

tape archiving is not suitable.

Is the technology available and at what cost?

Looking forward to a stimulating discussion.

Chris

Chris Gilpin

Biological Sciences Electron Microscope Unit

G452 Stopford Building

Oxford Road

Manchester

M13 9PT

phone +44 161 275 5170

fax +44 161 275 5171

http://www.biomed.man.ac.uk/biology/emunit/emhome.html

using a

writeable CD (CD-R). It is anyone's guess how long technology will be

around to

read the CDs, but seems the best bet at this time. DVDs are a coming

possibility for even more storage. The last blank CDs I bought were <$1.50

each. For 650 megs of storage, "that ain't bad".

Woody White, Electron Microscopist SEM/EDS/WDS

Work: Mcdermott Technology, Inc.

woody.n.white@mcdermott.com

http://www.mtiresearch.com/

Home: woody.white@worldnet.att.net

http://www.geocities.com/capecanaveral/3722

soul), I have done my best to come up with reasonable current market

pricing in all the following comparisons and this is a LONG email.

Yes, high resolution images (which maintain their resolution, i.e.

not subjected to 'losey-compresion') do take up alot of storage space

- as my students are constantly shocked at. Storage of these images

is problematic, and presently there is no ideal soloution, but here

are some for consideration:

Definitions: Mb= Megabit (Divide by 8 to get MB), MB = MegaByte,

GB=Gigabyte, 1000MB = 1GB (Hey some of us are really just starting

out) and $ = U.S.D.

In order to make some sense in comparison I have choosen the

simplistic view in regards to data transfer rates (i.e. the speed for

transfering data between the storage device and the computer

system/software) and simply have relied on manufacturers reported

transfer rates. Things to keep in mind with these numbers (1) you'll

never see these speeds in reality - they are all determined in ideal

situations not real world usage, but they are comparable with each

other; (2) Actual transfer rates will vary depending on the

interface used (i.e. the max. throughputs for the interfaces are

EIDE (1-10MB/sec) vs SCSI (5-10MB/sec) vs SCSI-Wide (20MB/Sec) vs

SCSI-UltraWide (40MB/Sec) vs parallel ports (<1 vs Fiber Coupling

(a.k.a. Fire Wire, 100+MB/Sec), (3) System configuration will also

effect this; i.e. what CPU, what BUS speed, how much memory (RAM)

what other components are in the system, what operating system, etc.

, (4) the biggest factor in the data transfer numbers game is

"Maximum Burst" transfer speed vs "Throughput speed". My only hope

in presenting this information is that is gives you a starting point

for comparisons.

1) Zip drives are cheap ($140 for drive) but cartridges are

expensive ($13 / 100MB - I'll use 100MB as the standard unit for

price comparison). 100MB is not very much storage capacity, and the

transfer speeds are very slow @ 1MB/Sec NOTE: unless you have min.

650MB free HD space you can NOT record an entire CD directly (On

-The-Fly) from a a zip drive, you'll have to record in multisession

mode (and lose 13MB in "overhead" for each session after the first

one, i.e. a 640MB CD-R would require 6 Sessions thus loosing 65 MB).

2) Iomega JAZ drives: $300/400 (Int/Ext) with 6.73MB/sec transfer, 1GB

cartridge@$124 [$12/100MB] (Expensive AND slow!)

3) Don't be so quick to reject tape storage. Tape storage can be

extremely cost effective in larger formats, speed can be a problem

but going back to older work-around solutions, users wishing to work

on files on Tuesday could transfer the data from tape to HD Monday

night, and then transfer back - alternately, utilizing a file server

for this task (File Server: HD's, Tape drives, CD-drives for

handleing just data storage: reading and writing only, no running of

other software) would free up workstations for computational work.

Yes, random access is limited but if you're looking at serial section

reconstruction you'll be accessing sequentially anyway. CON: You

have to a have a drive to read and write the data (unlike ubiquitous

CD-ROM readers).

Some general tech specs:

2GB drives ($600), 11MB/sec, tapes @ $10 [ $0.50/100MB]

2-4GB drives ($350-600), 29-42MB/sec, tapes @ $31-10

[$1.50-0.25/100MB] NOTE: Cheaper drives + More $ tapes

4-8GB drives ($750-1,200), 32-66MB/sec, Tapes @ $16-28 [$0.40

- 0.22/100 MB]

7-14GB drives ($700-1,600), 60-120MB/sec, tapes @ $16 [$0.22 -

0.11/100MB]

12-24GB drives ($1,000-1,300), 120-132MB/sec, tapes @ $32-42 [$0.35 -

0.13/100MB]

Drives go upto the following: 20-40GB, 32-64GB, 70-150GB, 100-200GB,

140-280GB @ $2,000-9,000.

NEW Iomega Ditto Max drives: upto 7GB* drives @ $200, upto 10GB*

drives @ $300, (*these are compressed data values, compression will

slow down transfer speeds) with transfer speeds upto 36MB/sec and

tapes running $20/3gb - $35/10GB [$0.20-$0.30/100MB].

4) CD-ROM storage: This makes alot of sense, since 99% of all

computers come with CD-ROM readers. If you (or your users) have

older CD-ROM readers, then they will need to cough up $80-150 to buy

a newer one (10x IDE drive - 16x SCSI). For comparison sake a 1x

refers to the standard speed of an Audio CD and allows for

150kilbytes of data transfered per second. Therefore a 10x CD-ROM

would allow for upto 1.5MB/second transfer. Actual transfer rates

will vary depending on the interface used (i.e. IDE vs SCSI, etc.).

CD-Recorders (CD-R's): these vary ALOT in recording speeds (1x-4x

-6x?) and prices follow ($340 - $800), plus you'll need recording

software ($50-100), and its recommended that you have a dedicated

temporary storage drive for the higher recording speeds ($180-500).

CD-R's are sensitive to recording errors, but they have become much

more routinely reliable in the last 1-2years (particularly with a

dedicated temp storage disk). CD-R's are WORM disks (Write Once

Read Many), that means if you record practice images, you can't

erase them and re-use the space. However, the recording media is

reasonably cheap @ 3.50-5.00/640MB disk [$0.54-0.78/100MB].

CD-ReWriteables (CD-RW): These are new to market as of this spring

they do allow for re-writing to the media. There are still only a

few manufactures and they record at 1-2x presently and cost ~$500.

The media is also very expensive ($25/disk) but is expected to drop

too reasonable prices by early next year. However! CD-RW's

apparently can only be read in CD-RW drives and NOT normal CD-ROM

drives. Ricoh does offer a drive which fuctions as CD-ROM, CD-R, and

CD-CW (MediaMaster ~$550).

5) DVD anyone? (and NO "DVD" is not a an anacronym, it once was but

had three different definitions so the powers that be decided to just

leave it as DVD). This ones easy: NOT READY FOR PRIME TIME YET.

Currently readers only are available, and recorders MIGHT be come

available late 1998, however the major manufactiring groups have had

a falling out again after coming up with a "standard" recording

format, and there are two incompatible (?) formats heading our way

so it might be until 1999-2000 before this becomes a

reality and affordable. However, it may offer the best solution to

todays image storage problems, in that the DVD storage capacity is

4.7GB for single sided and 7GB for double sided. But we shall see,

eh?

6) Optical Drives: Currently available optical dirves are

ReWritable (there are still some WORM drives though) fall into two

major categories: Mageneto-Optical (MO) drives and PD Drives. MO

drives come in various sizes from 128MB upto 4.6GB, I would suggest

that only drive 640MB and larger be considered. PD drives come in

640-650MB sizes, these sizes are very nice because they match the

CD-R size. Therefore you could use the MO or PD for temporary

storage and then archive to CD-R. However, once again you need to

have a drive to read these MO or PD's as well as write them. Most of

the drives will handle the next 2 or 3 sizes smaller capacity disks,

i.e. the 2.6GB MO's will read/write 1.3 & 650 disks. Prices are as

follows (Internal/External):

MO Drives:

640MB, $430/500, disks @ $30 [$4.68/100MB]

1.3GB , $1,200/1,300, disks @ $33 [$2.54/100MB]

2.6GB, $1,550/1,650, disks @ $45 [$1.73/100MB]

4.6GB, $1,450/1,550, disks @ $99 [$2.15/100MB]

[MediaStore has the Mitsubishi 4200 4.6GB on sale for $999!

4.2MB/sec transfer]

640/650 PD drives: $350/440, disk @ $34 [$5.20/100MB]

Toray has a 650 PD, 900kilobyte/sec which is also a CD-ROM reader for

$315/405.

7) Removable hard disk frames: Another alternative, one which has

been choosen by Hollywood (See Advanced Imaging October 1997, P.74)

is the usage of removable harddrives. Frames for making HD's

removable run: $20:IDE; $30:SCSI; $70:SCSI-Wide. However this does

not include the cost of the drive (obviously). Secondly, HD's are

delicate instruments and care must be taken when moving them about,

but a rack close to a user accessible computer system (say one with a

CD-Recorder?) would be a useful solution for the highest speed data

transfer. 2-6GB IDE's @ $7-5/100MB, 2-10GB SCSI @ $7-10/100MB,

2-23GB SCSI Ultra-Wides @ $7-20/100MB (On all HD's Bigger drives

have lowest costs per MB).

There are a few other, less common solutions, and each faclity will

need to develope their own prefered solution. However, I'm sure

there are a number of vendors out there who'd love to sell you a

turn-key system package for $20-40k.

Richard E. Edelmann, Ph.D.

Electron Microscopy Facility Supervisor

352 Pearson Hall

Miami University, Oxford, OH 45056

Ph: 513.529.5712 Fax: 513.529.4243

E-mail: edelmare@muohio.edu

experience, it is more likely that the above speeds are in MB/minute

instead of MB/second. That would place typical tape-drive speed more

in line with that of the Zip-drive. Also, most tape-drive software

accesses the tape in a sequential fashion, not randomly like the other

media. This means when you wish to relocate a particular file, it will

take a lot longer to get it from tape than from conventional media.

Jeff Ingeman Development Engineer

Department of Anatomy & Neurobiology

Department of Physiology & Biophysics

University of California - Irvine

(714) 824-7536

jingeman@uci.edu

jingeman@aol.com

jingeman@yahoo.com

the CD's be written in a standard format that can be read at any speed?? I

am about to buy a CD writer and apparently have missed something here.

TIA, Tom

Thomas E. Phillips, Ph.D.

Associate Professor of Biological Sciences

Director, Molecular Cytology Core Facility

3 Tucker Hall

University of Missouri

Columbia, MO 65211

(573)-882-4712 (voice)

(573)-882-0123 (fax)

tphillips@biosci.mbp.missouri.edu

upgrade the older 1X to 4X units to the faster speeds. I worked with a 1X

for a few years. It was better than nothing, but it was slow!

Now a question for Richard. Do the tape drives really achieve 20 MB/sec or

did you mean 20 MB/min? Our Ditto 2GB is on a flopy port and is doing well

if it does 10 MB/min.

----------------------------------------------------

Warren E. Straszheim

23 Town Engineering

Iowa State University

Ames IA, 50011

Phone: 515-294-8187 FAX: 515-294-8216

E-Mail: wesaia@iastate.edu (or: wes@ameslab.gov)

http://www.marl.iastate.edu/marl/ (re: SEM)

http://www.public.iastate.edu/~iprt_info/cfce/ (re: coal)

on 1X CD readers. I have even encountered some 2X drives that don't like

the written discs. (Discs are written at 1x speed.) We have 2 writers and

the same holds true for CDs written by either drive. Never had a problem

with a 4X or higher reader.

Bob Holthausen

Pall Corporation

Port Washington, NY

Bob_Holthausen@Pall.com

Here is my (short)experience on CDR.

I have a Sony CDR 928 on IDE Bus ( all my system is IDE not SCSI)and the

first pb I encounter is that my old Windows95 version never never recognize

this CDR. So I installed an OSR2 version on a new disk and all was OK.

The software is easy CD pro from adaptec (upgraded for IDE). First writing

(600Mo) no problem but impossible to read the datas on my 1 years old CD

8x. I check on many other even on a very old 2x Mitsumi and all was OK.

So I change for a 24x Pionneer (the CDs were from Sony).

All that takes at least one week late at night!

My conclusions are the following:

Writting speed doesn't affect reading, it's just a safety, the slower the

safest.

Never use Multisession, the price of CDs is now as low as 2$ and doesn't

justify that.

I use different manufacturer for CDs (SONY TRAXDATA...) without PB.

You can never be sure that your work can be read on all CD for example

I've made an Audio which is readable by all CD except on a JVC CD!

I enclose a part of my Easy CD pro user's manual that prove that

manufacturers know the problem.

I have no interrest in any of the above company (just problem with some!)

and this is my personnal opinion.

If more information needed pls Email me.

FROM EASY CD PRO VERSION 2.0 ADAPTEC USER'S GUIDE

Problems Reading Recordable CDs

If you have successfully written a CD but have problems reading it,

there are a number of possible reasons :

* If the CD can be read on the CD recorder but not on a standard CD-ROM

drive, check in Disc Info and Tools to make sure that the session

containing the data you just wrote is closed. CD-ROM drives cannot read

data from a session which is not closed.

• If your CD is ejected, or you receive an error message, or you have

random problems accessing files from the CD, the problem may be that your

CD-ROM drive is not well calibrated to read recordable CDs.

a If you recorded the CD using the DOS filenames option in the File Names

tab, but there are nonetheless difficulties in reading back the CD on DOS

or Windows OR 3.1 system, it may be that you have an older version of

MSCDEX (before version 2.23) on your system.

Problems Reading Multisession CDs

If you can see only data recorded in the first session on the CD but not in

subsequent sessions, it may be that

• You recorded the CD in CD-ROM (Mode 1) format, while your multisession

CD-ROM drive only recognizes CD-ROM XA (Mode 2) multisession CDs.

or,

• Your CD-ROM drive does not support muti session at all.

If you can see only data recorded in the last session, you may have

forgotten to link your new data with data previously recorded on the CD.

Make sure to select a track in the Load Contents tab before recording.

CD-ROM Drive Incompatibility with Recordable CDs

Sometimes, it appears that you wrote a CD without trouble and can read it

on your CD recorder ; however, when you put it in a standard CD-ROM drive,

the CD is ejected, or you get error messages such as no CD-ROM or not ready

reading, or you have random problems accessing some files or directories.

You may find that the problems vanish completely when reading the CD on a

different CD-ROM drive.

This maybe due to compatibility problems with some CD-ROM drives,

especially older ones, and recordable CDs. Some CD-ROM drives' lasers are

not calibrated to read recordable CDs, whose surface is different from that

of factory-pressed CDs. If your CD-ROM drive reads mass-produced (silver)

CDs but not recordable CDs, check with the CD-ROM drive manufacture to

determine whether this is the problem. In some cases , an upgrade is

available which will solve the problem.

The combination of CD brand and CD recorder can make a difference. Use CD

media recommended by your CD recorder manufacturer.

==========================================================

Jacky Larnould

mailto:larnould@worlnet.fr

voice:33 (0)4 67 72 28 26

fax :33 (0)4 67 79 54 90

grey, 24 bit RGB, z-series etc.) and I was wondering whether

there is

some relatively cheap software/shareware around that I could use

to

catalogue the images. I want to be able to save some information

with

the images and thumnail sketches would be useful.

Alternatively, if someone knows how I can use Microsoft Access as

an

image database without having to embed the full resolution

picture in

each record I would be grateful.

Any ideas? contact Mark Auty

Mark Auty

DPC Moorepark

Fermoy

Co. Cork

Ireland

I use Thumbs Plus (approx. $60 US if I remember correctly)

Cerious Software, Inc.

1515 Mockingbird Lande

Suite 209

Charlotte, NC 28209

http://www.cerious.com

I have no financial interest in this company other than doing my part as

a very satisfied customer.

Crossman, Harold

crossman@OSI.SYLVANIA.com

tool. It provides a thumbnail of all images in a directory.

Jay Jerome

jjerome@bgsm.edu

Company Cerious Software Inc. http://cerious.catalogue.com/index.html

has a great software ThumbPlus 3.0 for 60 US$.

Henrik Kaker

SEM-EDS Laboratory

Metal Ravne d.o.o.

Slovenia

position, I've just gotten 5 concurrent site licenses for myself and my

team. I don't know how good their Mac version is. I believe that it is

still in beta testing. It is shareware and Cerious software has a website

where you can download the shareware version. Once you are registered,

there are some things that are available, but the unregistered version is

very good. I tried it out that way after it was suggested previously on the

Microscopy Listserver.

-Scott Walck

I've been using a product called imageAXS CE v3.0. This is a free version of

a slightly more flexible commercial program. It automatically finds image

files and creates a MS Access database which you can edit and use for

searching and indexing images. the url is:

http://www.dascorp.com

Hope this helps glenn

Glenn Poirier Tel (514) 398 -6774

Electron Microprobe Laboratory Fax (514) 398 4680

Earth and Planetary Sciences glennp@stoner.eps.mcgill.ca

McGill University

http://castaing.eps.mcgill.ca

3450 University St.

Montreal, Qc H3A 2A7

system. It has pretty powerful report generation software which allows you

to effectively replace traditioinal film in the photo documentation

process. Going digital seems to pay for itself quickly. The other good

thing is that it has network software, so you can access the database of

images from your desktop PC's.

They are at www.mis-hq.com.

Seth J. Grotelueschen

sethg@CompuServe.COM